├── .gitignore ├── .gitmodules ├── LICENSE ├── README.md ├── VERSION.info ├── container └── apptainer │ ├── MCScanX.def │ ├── angsd.def │ ├── casoffinder.def │ ├── kallisto.def │ ├── macs3.def │ ├── plink19.def │ ├── plink20.def │ ├── seidr.def │ ├── swarm.def │ ├── tagdust.def │ └── velocyto.def ├── nextflow ├── config │ └── upscb.config ├── seidr │ ├── nextflow.config │ └── vala.nf └── template │ ├── rnaseq_T89_v1.json │ ├── rnaseq_arabidopsis_araport11.json │ ├── rnaseq_lupin_v1.json │ ├── rnaseq_lupin_v2.json │ ├── rnaseq_microtom_shirasawa.json │ ├── rnaseq_microtom_xue.json │ ├── rnaseq_spruce_v2.json │ └── rnaseq_tomato_v4.json ├── pipeline ├── join_targets.sh ├── runAbyssBloom.sh ├── runAbyssScaffold.sh ├── runAlevin.sh ├── runAlignReads.sh ├── runAmpliconSeqPreprocessing.sh ├── runAmpliconSequencingPipeline.sh ├── runAnova.sh ├── runAsArray.sh ├── runAssemblathonStat.sh ├── runBAMtoCRAM.sh ├── runBESST-RNA.sh ├── runBESST.sh ├── runBWA.sh ├── runBamSubset.sh ├── runBamtoFastQ.sh ├── runBedToolsBamToFastq.sh ├── runBedToolsCoverage.sh ├── runBedToolsGCov.sh ├── runBedToolsIntersect.sh ├── runBedToolsSubtract.sh ├── runBgzipTabix.sh ├── runBismark.sh ├── runBlastFormatDb.sh ├── runBlastPlus.sh ├── runBlastPlus2.sh ├── runBlastPlusMakeblastdb.sh ├── runBlastPlusXML.sh ├── runBlastPlusXMLasArray.sh ├── runBowtie.sh ├── runBowtie2.sh ├── runBuscoPlant.sh ├── runBwaIndex.sh ├── runBwamem.sh ├── runBwasw.sh ├── runCLARK.sh ├── runCLR.sh ├── runCNCI.sh ├── runCPC2.sh ├── runCdHitEst.sh ├── runCdhit.sh ├── runCleanTrinity.sh ├── runCmd.sh ├── runCreateDEXSeqReference.sh ├── runCuffcompare.sh ├── runCufflinks.sh ├── runCuffmerge.sh ├── runCutadapt.sh ├── runDISCOVARdeNovo.sh ├── runDeML.sh ├── runDemultiplex.sh ├── runDexSeqCount.sh ├── runDiamond.sh ├── runDiamond4B2G0.sh ├── runDiamondMakedb.sh ├── runDigitalNormalization.sh ├── runDocker.sh ├── runFLASH.sh ├── runFRC.sh ├── runFastQC.sh ├── runFastQCCounts.sh ├── runFastQCMultiviewer.sh ├── runFastQValidator.sh ├── runFindlncRNA_pipeline.sh ├── runFrameDP.sh ├── runFusionFilterDataset.sh ├── runFusionInspector.sh ├── runFusionMap.sh ├── runGATK_CombineGVCFs.sh ├── runGATK_CombineVariants.sh ├── runGATK_GenotypeGVCFs.sh ├── runGATK_HaplotypeCaller.sh ├── runGATK_IndelRealigner.sh ├── runGATK_SplitNCigarReads.sh ├── runGATK_UnifiedGenotyper.sh ├── runGATK_VariantFiltration.sh ├── runGENIE3.sh ├── runGMAP.sh ├── runGMAPIndex.sh ├── runGMAPasArray.sh ├── runGROM.sh ├── runGatkFastaAlternateReferenceMaker.sh ├── runGatkPreprocessing.sh ├── runGatkRealignerTargetCreator.sh ├── runGatk_BaseRecalibration.sh ├── runGeneNetworkRAggregate.sh ├── runGeneNetworkRPreparation.sh ├── runGeneNetworkRRun.sh ├── runGeneNetworkRThreshold.sh ├── runGenepair.sh ├── runGenerateCountfiles.sh ├── runGenomeTools.sh ├── runGetPasaFasta.sh ├── runGffRead.sh ├── runGmapl.sh ├── runGzip.sh ├── runHTSeq.sh ├── runHTSeqStats.sh ├── runHmmScan.sh ├── runITSx.sh ├── runInfomap.sh ├── runJBrowse2.sh ├── runJellyfishBc.sh ├── runJellyfishCount.sh ├── runJellyfishHisto.sh ├── runKallisto.sh ├── runKallistoIndex.sh ├── runKallistoStats.sh ├── runKmergenie.sh ├── runKnitR.sh ├── runLoadPasaGenome.sh ├── runMacs2.sh ├── runMacs2_bdgcmp.sh ├── runMacs2_broad.sh ├── runMacs2_broad_noC.sh ├── runMarkDuplicates.sh ├── runMeme.sh ├── runMemeChip.sh ├── runMerger.sh ├── runMetaxa2.sh ├── runMiRBase_SS.sh ├── runMinimap2.sh ├── runMinion.sh ├── runMiso.sh ├── runMisoPeDistribution.sh ├── runMmseq.sh ├── runMmseqFromFastq.sh ├── runMultiQC.sh ├── runMummer.sh ├── runMuscle.sh ├── runNarromi.sh ├── runNutil.sh ├── runOSA.sh ├── runPASA_GFF3_validator.sh ├── runPLEK.sh ├── runPLncPRO.sh ├── runParseMacs2.sh ├── runPasaAlignment.sh ├── runPasaCompare.sh ├── runPasaComprehensiveTranscriptomeBuilder.sh ├── runPasaLoadAnnotation.sh ├── runPasaSeqclean.sh ├── runPasaSupportingEvidenceAlignment.sh ├── runPasaValidAnnotationUpdate.sh ├── runPearsonSpearmanCorrelation.sh ├── runPicardAddOrReplaceReadGroups.sh ├── runPicardCreateSequenceDictionary.sh ├── runPicardMarkDuplicatesWithMateCigar.sh ├── runPicardSamToFastq.sh ├── runPlaac.sh ├── runPrepInfomap.sh ├── runProjectCreation.sh ├── runProjectPermission.sh ├── runProjectSetup.sh ├── runPyfasta.sh ├── runPythonLncRNAFiltering.py ├── runQCprot.sh ├── runR.sh ├── runRNASeqGATKPreprocessing.sh ├── runRNASeqPreprocessing.sh ├── runRNASeqSEPreprocessing.sh ├── runRePair.sh ├── runReaper.sh ├── runRemoveBlankLines.sh ├── runRepeatMasker.sh ├── runRepeatModeler.sh ├── runRiboSeqSePreprocessing.sh ├── runRmarkdown.sh ├── runRnaSeqPipelineStats.sh ├── runRscript.sh ├── runSRnaWorkBenchFilter.sh ├── runSSPACE-LR.sh ├── runSTAR.sh ├── runSTARGenomeGenerate.sh ├── runSTARGenomeLoad.sh ├── runSTARGenomeRemove.sh ├── runSTARStats.sh ├── runSTAR_trx.sh ├── runSUPPA2DiffSplice.sh ├── runSUPPA2GenerateEvents.sh ├── runSUPPA2PsiPerEvent.sh ├── runSUPPA2PsiPerIsoform.sh ├── runSalmon.py ├── runSalmon.sh ├── runSalmonIndex.sh ├── runSalmonSE.sh ├── runSalmonStats.sh ├── runSampleN.sh ├── runSampleN_SE.sh ├── runSamtoolsFaidx.sh ├── runSamtoolsFlagstat.sh ├── runSamtoolsIdxstats.sh ├── runSamtoolsIndex.sh ├── runSamtoolsMerge.sh ├── runSamtoolsReheader.sh ├── runSamtoolsSort.sh ├── runSamtools_miRNAclusters.sh ├── runSamtools_split_primary.sh ├── runSeidrAggregate.sh ├── runSeidrBackbone.sh ├── runSeidrRoc.sh ├── runSeidrThreshold.sh ├── runShortstack.sh ├── runSnpEff.sh ├── runSnpEffBuild.sh ├── runSortmerna.sh ├── runSortmernaDennis.sh ├── runSortmernaMtSSU.sh ├── runSortmernaStats.sh ├── runSraFastqDump.sh ├── runStarBamAndUnmappedToFastq.sh ├── runStarFusion.sh ├── runSwestoreSync.sh ├── runTIGLM.sh ├── runTaxonomicClassification.sh ├── runTaxonomyUpdate.sh ├── runThresholdNetwork.sh ├── runTransfer.sh ├── runTremulaTranslate.sh ├── runTrim.sh ├── runTrimmomatic.sh ├── runTrimmomaticSeStats.sh ├── runTrimmomaticStats.sh ├── runTrinity.sh ├── runTrinityEstimateExpression.sh ├── runTrinityGenomeGuided.sh ├── runTrinitySE.sh ├── runTrinityTransDecoder.sh ├── runUpdateNCBI.sh ├── runUsearch.sh ├── runVCFPlot.sh ├── runVCFStats.sh ├── runVsearch.sh ├── runVsearchDatabase.sh ├── runVsearchMergePairs.sh ├── runXxhashsum.sh ├── run_ClustalW.sh ├── run_HMMbuild.sh ├── run_array_pseudopipe.sh ├── run_array_repeatmasker.sh ├── run_array_repeatmasker2.sh ├── run_array_repeatmasker2coredump.sh ├── run_check_offtarget_for_guide_RNAs.sh ├── run_makeblastdb_pglauca.sh ├── run_makeblastdb_ptaeda.sh ├── run_ppfinder.sh ├── run_psari.sh ├── run_pseudopipe.sh ├── run_psf.sh ├── sortMeRnaV2Stats.sh ├── submit_nextflow_RNAseq.sh ├── the_master.sh ├── the_master_beta.sh └── the_master_v2.sh ├── src ├── R │ ├── ARACNE.R │ ├── GENIE3_simple.R │ ├── GeneNet.R │ ├── Rmodules.R │ ├── TIGLM.R │ ├── TIGRESS.R │ ├── WgcnaClusterPlot.R │ ├── amplicon_basics.R │ ├── blastUtilities.R │ ├── cigarUtility.R │ ├── convertTemplates.R │ ├── createGeneAnnotation.R │ ├── createGeneModelGff.R │ ├── createMapFileForDeML.R │ ├── createSyntheticTranscripts.R │ ├── csawUtilities.R │ ├── densityPlot.R │ ├── deviseSequenceFromGFF.R │ ├── enaCsvEdit.R │ ├── expressionSpecificityUtility.R │ ├── expressionSpecificityUtility.html │ ├── extractGff3Subset.R │ ├── extractPromoter_Template_.R │ ├── featureSelection.R │ ├── featureSelection.html │ ├── functions_DifferentialExpression.R │ ├── functions_GOenrichment_TopGO.R │ ├── functions_ancombc.R │ ├── genericRnaSeq.R │ ├── genericRnaSeq.html │ ├── getCoverage.R │ ├── gff3Utilities.R │ ├── gff3Utilities.html │ ├── ggComparisonplot.R │ ├── gmapUtilities.R │ ├── gopher.R │ ├── gopher2-example.R │ ├── mailR.R │ ├── metageneUtilities.R │ ├── methylKitPCA_withVar.R │ ├── methylation_utils.R │ ├── misoPePlot.R │ ├── parseUniRef90IDs.R │ ├── parse_gmap.R │ ├── pasaUtilities.R │ ├── pasaUtilities.html │ ├── percentile.R │ ├── pfamUtilities.R │ ├── plot.alphabetByCycle.R │ ├── plot.multidensity.R │ ├── plotClusterNetwork.R │ ├── plotDispLSD.R │ ├── plotEnrichedTreemap.R │ ├── plotMA.R │ ├── plotSft.R │ ├── plotVCFQual.R │ ├── plotVennDiagram.R │ ├── pseudoChromosomeUtilities.R │ ├── rePairFastq.R │ ├── reverseFastq.R │ ├── rfam5SKrakenPrep.R │ ├── rmd.R │ ├── salmonPEplusSE.R │ ├── salmonPEplusSE.html │ ├── salmonUtilities.R │ ├── sequenceUtilities.R │ ├── sequenceUtilities.html │ ├── topGoUtilities.R │ ├── topGoUtilities.html │ ├── try opt.R │ ├── updateAspenVcfv1.0.R │ ├── updateTaxonomyDivisionTable.R │ └── volcanoPlot.R ├── bash │ ├── 23s_silva_installation.sh │ ├── 5S_rfam_installation.sh │ ├── functions.sh │ ├── oneliners.md │ ├── seidr-aggregate-kebnekaise.sh │ ├── seidr-aracne.sh │ ├── seidr-elnet-wrapper-kebnekaise.sh │ ├── seidr-elnet-wrapper.sh │ ├── seidr-import-kebnekaise.sh │ ├── seidr-import-micro.sh │ ├── seidr-wrapper-kebnekaise.sh │ ├── seidr-wrapper-micro.sh │ ├── try-catch-example.sh │ ├── try-catch.sh │ └── updateTaxonomySqlite.sh └── python │ ├── fastQCmultiviewer.py │ └── generate_import_script.py └── templates ├── R ├── BiologicalQA.R ├── BiologicalQA.Rmd ├── DE_template.Rmd ├── DifferentialAbundance_ANCOMBC2_tentative.qmd ├── DifferentialExpression.R ├── DifferentialExpression_WithGOenrichment.Rmd ├── Mfuzz.R ├── Network_Clustering_with_Leiden.R ├── README.md ├── WorkInProgress_DifferentialExpression_WithAllEnrichment.qmd ├── bulogo2.png ├── empty.R ├── footer.html ├── header.html ├── seidrFirstDegreeNeighbour.R ├── seidrPageRank.R ├── seidrPreparation.R ├── seidrRoc.R └── style.css ├── bash ├── cleanup.sh ├── runTemplate.sh ├── submitSeidrAggregate.sh ├── submitSeidrBackbone.sh ├── submitSeidrRoc.sh └── template.sh └── python └── Network_Clustering_with_Leiden.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/.gitignore -------------------------------------------------------------------------------- /.gitmodules: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/README.md -------------------------------------------------------------------------------- /VERSION.info: -------------------------------------------------------------------------------- 1 | UPSCb-common: 1.2.1 2 | -------------------------------------------------------------------------------- /container/apptainer/MCScanX.def: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/container/apptainer/MCScanX.def -------------------------------------------------------------------------------- /container/apptainer/angsd.def: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/container/apptainer/angsd.def -------------------------------------------------------------------------------- /container/apptainer/casoffinder.def: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/container/apptainer/casoffinder.def -------------------------------------------------------------------------------- /container/apptainer/kallisto.def: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/container/apptainer/kallisto.def -------------------------------------------------------------------------------- /container/apptainer/macs3.def: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/container/apptainer/macs3.def -------------------------------------------------------------------------------- /container/apptainer/plink19.def: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/container/apptainer/plink19.def -------------------------------------------------------------------------------- /container/apptainer/plink20.def: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/container/apptainer/plink20.def -------------------------------------------------------------------------------- /container/apptainer/seidr.def: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/container/apptainer/seidr.def -------------------------------------------------------------------------------- /container/apptainer/swarm.def: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/container/apptainer/swarm.def -------------------------------------------------------------------------------- /container/apptainer/tagdust.def: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/container/apptainer/tagdust.def -------------------------------------------------------------------------------- /container/apptainer/velocyto.def: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/container/apptainer/velocyto.def -------------------------------------------------------------------------------- /nextflow/config/upscb.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/nextflow/config/upscb.config -------------------------------------------------------------------------------- /nextflow/seidr/nextflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/nextflow/seidr/nextflow.config -------------------------------------------------------------------------------- /nextflow/seidr/vala.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/nextflow/seidr/vala.nf -------------------------------------------------------------------------------- /nextflow/template/rnaseq_T89_v1.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/nextflow/template/rnaseq_T89_v1.json -------------------------------------------------------------------------------- /nextflow/template/rnaseq_arabidopsis_araport11.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/nextflow/template/rnaseq_arabidopsis_araport11.json -------------------------------------------------------------------------------- /nextflow/template/rnaseq_lupin_v1.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/nextflow/template/rnaseq_lupin_v1.json -------------------------------------------------------------------------------- /nextflow/template/rnaseq_lupin_v2.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/nextflow/template/rnaseq_lupin_v2.json -------------------------------------------------------------------------------- /nextflow/template/rnaseq_microtom_shirasawa.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/nextflow/template/rnaseq_microtom_shirasawa.json -------------------------------------------------------------------------------- /nextflow/template/rnaseq_microtom_xue.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/nextflow/template/rnaseq_microtom_xue.json -------------------------------------------------------------------------------- /nextflow/template/rnaseq_spruce_v2.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/nextflow/template/rnaseq_spruce_v2.json -------------------------------------------------------------------------------- /nextflow/template/rnaseq_tomato_v4.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/nextflow/template/rnaseq_tomato_v4.json -------------------------------------------------------------------------------- /pipeline/join_targets.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/join_targets.sh -------------------------------------------------------------------------------- /pipeline/runAbyssBloom.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runAbyssBloom.sh -------------------------------------------------------------------------------- /pipeline/runAbyssScaffold.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runAbyssScaffold.sh -------------------------------------------------------------------------------- /pipeline/runAlevin.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runAlevin.sh -------------------------------------------------------------------------------- /pipeline/runAlignReads.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runAlignReads.sh -------------------------------------------------------------------------------- /pipeline/runAmpliconSeqPreprocessing.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runAmpliconSeqPreprocessing.sh -------------------------------------------------------------------------------- /pipeline/runAmpliconSequencingPipeline.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runAmpliconSequencingPipeline.sh -------------------------------------------------------------------------------- /pipeline/runAnova.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runAnova.sh -------------------------------------------------------------------------------- /pipeline/runAsArray.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runAsArray.sh -------------------------------------------------------------------------------- /pipeline/runAssemblathonStat.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runAssemblathonStat.sh -------------------------------------------------------------------------------- /pipeline/runBAMtoCRAM.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runBAMtoCRAM.sh -------------------------------------------------------------------------------- /pipeline/runBESST-RNA.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runBESST-RNA.sh -------------------------------------------------------------------------------- /pipeline/runBESST.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runBESST.sh -------------------------------------------------------------------------------- /pipeline/runBWA.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runBWA.sh -------------------------------------------------------------------------------- /pipeline/runBamSubset.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runBamSubset.sh -------------------------------------------------------------------------------- /pipeline/runBamtoFastQ.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runBamtoFastQ.sh -------------------------------------------------------------------------------- /pipeline/runBedToolsBamToFastq.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runBedToolsBamToFastq.sh -------------------------------------------------------------------------------- /pipeline/runBedToolsCoverage.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runBedToolsCoverage.sh -------------------------------------------------------------------------------- /pipeline/runBedToolsGCov.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runBedToolsGCov.sh -------------------------------------------------------------------------------- /pipeline/runBedToolsIntersect.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runBedToolsIntersect.sh -------------------------------------------------------------------------------- /pipeline/runBedToolsSubtract.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runBedToolsSubtract.sh -------------------------------------------------------------------------------- /pipeline/runBgzipTabix.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runBgzipTabix.sh -------------------------------------------------------------------------------- /pipeline/runBismark.sh: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /pipeline/runBlastFormatDb.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runBlastFormatDb.sh -------------------------------------------------------------------------------- /pipeline/runBlastPlus.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runBlastPlus.sh -------------------------------------------------------------------------------- /pipeline/runBlastPlus2.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runBlastPlus2.sh -------------------------------------------------------------------------------- /pipeline/runBlastPlusMakeblastdb.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runBlastPlusMakeblastdb.sh -------------------------------------------------------------------------------- /pipeline/runBlastPlusXML.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runBlastPlusXML.sh -------------------------------------------------------------------------------- /pipeline/runBlastPlusXMLasArray.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runBlastPlusXMLasArray.sh -------------------------------------------------------------------------------- /pipeline/runBowtie.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runBowtie.sh -------------------------------------------------------------------------------- /pipeline/runBowtie2.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runBowtie2.sh -------------------------------------------------------------------------------- /pipeline/runBuscoPlant.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runBuscoPlant.sh -------------------------------------------------------------------------------- /pipeline/runBwaIndex.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runBwaIndex.sh -------------------------------------------------------------------------------- /pipeline/runBwamem.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runBwamem.sh -------------------------------------------------------------------------------- /pipeline/runBwasw.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runBwasw.sh -------------------------------------------------------------------------------- /pipeline/runCLARK.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runCLARK.sh -------------------------------------------------------------------------------- /pipeline/runCLR.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runCLR.sh -------------------------------------------------------------------------------- /pipeline/runCNCI.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runCNCI.sh -------------------------------------------------------------------------------- /pipeline/runCPC2.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runCPC2.sh -------------------------------------------------------------------------------- /pipeline/runCdHitEst.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runCdHitEst.sh -------------------------------------------------------------------------------- /pipeline/runCdhit.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runCdhit.sh -------------------------------------------------------------------------------- /pipeline/runCleanTrinity.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runCleanTrinity.sh -------------------------------------------------------------------------------- /pipeline/runCmd.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runCmd.sh -------------------------------------------------------------------------------- /pipeline/runCreateDEXSeqReference.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runCreateDEXSeqReference.sh -------------------------------------------------------------------------------- /pipeline/runCuffcompare.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runCuffcompare.sh -------------------------------------------------------------------------------- /pipeline/runCufflinks.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runCufflinks.sh -------------------------------------------------------------------------------- /pipeline/runCuffmerge.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runCuffmerge.sh -------------------------------------------------------------------------------- /pipeline/runCutadapt.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runCutadapt.sh -------------------------------------------------------------------------------- /pipeline/runDISCOVARdeNovo.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runDISCOVARdeNovo.sh -------------------------------------------------------------------------------- /pipeline/runDeML.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runDeML.sh -------------------------------------------------------------------------------- /pipeline/runDemultiplex.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runDemultiplex.sh -------------------------------------------------------------------------------- /pipeline/runDexSeqCount.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runDexSeqCount.sh -------------------------------------------------------------------------------- /pipeline/runDiamond.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runDiamond.sh -------------------------------------------------------------------------------- /pipeline/runDiamond4B2G0.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runDiamond4B2G0.sh -------------------------------------------------------------------------------- /pipeline/runDiamondMakedb.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runDiamondMakedb.sh -------------------------------------------------------------------------------- /pipeline/runDigitalNormalization.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runDigitalNormalization.sh -------------------------------------------------------------------------------- /pipeline/runDocker.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runDocker.sh -------------------------------------------------------------------------------- /pipeline/runFLASH.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runFLASH.sh -------------------------------------------------------------------------------- /pipeline/runFRC.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runFRC.sh -------------------------------------------------------------------------------- /pipeline/runFastQC.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runFastQC.sh -------------------------------------------------------------------------------- /pipeline/runFastQCCounts.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runFastQCCounts.sh -------------------------------------------------------------------------------- /pipeline/runFastQCMultiviewer.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runFastQCMultiviewer.sh -------------------------------------------------------------------------------- /pipeline/runFastQValidator.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runFastQValidator.sh -------------------------------------------------------------------------------- /pipeline/runFindlncRNA_pipeline.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runFindlncRNA_pipeline.sh -------------------------------------------------------------------------------- /pipeline/runFrameDP.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runFrameDP.sh -------------------------------------------------------------------------------- /pipeline/runFusionFilterDataset.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runFusionFilterDataset.sh -------------------------------------------------------------------------------- /pipeline/runFusionInspector.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runFusionInspector.sh -------------------------------------------------------------------------------- /pipeline/runFusionMap.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runFusionMap.sh -------------------------------------------------------------------------------- /pipeline/runGATK_CombineGVCFs.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runGATK_CombineGVCFs.sh -------------------------------------------------------------------------------- /pipeline/runGATK_CombineVariants.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runGATK_CombineVariants.sh -------------------------------------------------------------------------------- /pipeline/runGATK_GenotypeGVCFs.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runGATK_GenotypeGVCFs.sh -------------------------------------------------------------------------------- /pipeline/runGATK_HaplotypeCaller.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runGATK_HaplotypeCaller.sh -------------------------------------------------------------------------------- /pipeline/runGATK_IndelRealigner.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runGATK_IndelRealigner.sh -------------------------------------------------------------------------------- /pipeline/runGATK_SplitNCigarReads.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runGATK_SplitNCigarReads.sh -------------------------------------------------------------------------------- /pipeline/runGATK_UnifiedGenotyper.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runGATK_UnifiedGenotyper.sh -------------------------------------------------------------------------------- /pipeline/runGATK_VariantFiltration.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runGATK_VariantFiltration.sh -------------------------------------------------------------------------------- /pipeline/runGENIE3.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runGENIE3.sh -------------------------------------------------------------------------------- /pipeline/runGMAP.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runGMAP.sh -------------------------------------------------------------------------------- /pipeline/runGMAPIndex.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runGMAPIndex.sh -------------------------------------------------------------------------------- /pipeline/runGMAPasArray.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runGMAPasArray.sh -------------------------------------------------------------------------------- /pipeline/runGROM.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runGROM.sh -------------------------------------------------------------------------------- /pipeline/runGatkFastaAlternateReferenceMaker.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runGatkFastaAlternateReferenceMaker.sh -------------------------------------------------------------------------------- /pipeline/runGatkPreprocessing.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runGatkPreprocessing.sh -------------------------------------------------------------------------------- /pipeline/runGatkRealignerTargetCreator.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runGatkRealignerTargetCreator.sh -------------------------------------------------------------------------------- /pipeline/runGatk_BaseRecalibration.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runGatk_BaseRecalibration.sh -------------------------------------------------------------------------------- /pipeline/runGeneNetworkRAggregate.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runGeneNetworkRAggregate.sh -------------------------------------------------------------------------------- /pipeline/runGeneNetworkRPreparation.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runGeneNetworkRPreparation.sh -------------------------------------------------------------------------------- /pipeline/runGeneNetworkRRun.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runGeneNetworkRRun.sh -------------------------------------------------------------------------------- /pipeline/runGeneNetworkRThreshold.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runGeneNetworkRThreshold.sh -------------------------------------------------------------------------------- /pipeline/runGenepair.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runGenepair.sh -------------------------------------------------------------------------------- /pipeline/runGenerateCountfiles.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runGenerateCountfiles.sh -------------------------------------------------------------------------------- /pipeline/runGenomeTools.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runGenomeTools.sh -------------------------------------------------------------------------------- /pipeline/runGetPasaFasta.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runGetPasaFasta.sh -------------------------------------------------------------------------------- /pipeline/runGffRead.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runGffRead.sh -------------------------------------------------------------------------------- /pipeline/runGmapl.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runGmapl.sh -------------------------------------------------------------------------------- /pipeline/runGzip.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runGzip.sh -------------------------------------------------------------------------------- /pipeline/runHTSeq.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runHTSeq.sh -------------------------------------------------------------------------------- /pipeline/runHTSeqStats.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runHTSeqStats.sh -------------------------------------------------------------------------------- /pipeline/runHmmScan.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runHmmScan.sh -------------------------------------------------------------------------------- /pipeline/runITSx.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runITSx.sh -------------------------------------------------------------------------------- /pipeline/runInfomap.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runInfomap.sh -------------------------------------------------------------------------------- /pipeline/runJBrowse2.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runJBrowse2.sh -------------------------------------------------------------------------------- /pipeline/runJellyfishBc.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runJellyfishBc.sh -------------------------------------------------------------------------------- /pipeline/runJellyfishCount.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runJellyfishCount.sh -------------------------------------------------------------------------------- /pipeline/runJellyfishHisto.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runJellyfishHisto.sh -------------------------------------------------------------------------------- /pipeline/runKallisto.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runKallisto.sh -------------------------------------------------------------------------------- /pipeline/runKallistoIndex.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runKallistoIndex.sh -------------------------------------------------------------------------------- /pipeline/runKallistoStats.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runKallistoStats.sh -------------------------------------------------------------------------------- /pipeline/runKmergenie.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runKmergenie.sh -------------------------------------------------------------------------------- /pipeline/runKnitR.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runKnitR.sh -------------------------------------------------------------------------------- /pipeline/runLoadPasaGenome.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runLoadPasaGenome.sh -------------------------------------------------------------------------------- /pipeline/runMacs2.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runMacs2.sh -------------------------------------------------------------------------------- /pipeline/runMacs2_bdgcmp.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runMacs2_bdgcmp.sh -------------------------------------------------------------------------------- /pipeline/runMacs2_broad.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runMacs2_broad.sh -------------------------------------------------------------------------------- /pipeline/runMacs2_broad_noC.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runMacs2_broad_noC.sh -------------------------------------------------------------------------------- /pipeline/runMarkDuplicates.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runMarkDuplicates.sh -------------------------------------------------------------------------------- /pipeline/runMeme.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runMeme.sh -------------------------------------------------------------------------------- /pipeline/runMemeChip.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runMemeChip.sh -------------------------------------------------------------------------------- /pipeline/runMerger.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runMerger.sh -------------------------------------------------------------------------------- /pipeline/runMetaxa2.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runMetaxa2.sh -------------------------------------------------------------------------------- /pipeline/runMiRBase_SS.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runMiRBase_SS.sh -------------------------------------------------------------------------------- /pipeline/runMinimap2.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runMinimap2.sh -------------------------------------------------------------------------------- /pipeline/runMinion.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runMinion.sh -------------------------------------------------------------------------------- /pipeline/runMiso.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runMiso.sh -------------------------------------------------------------------------------- /pipeline/runMisoPeDistribution.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runMisoPeDistribution.sh -------------------------------------------------------------------------------- /pipeline/runMmseq.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runMmseq.sh -------------------------------------------------------------------------------- /pipeline/runMmseqFromFastq.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runMmseqFromFastq.sh -------------------------------------------------------------------------------- /pipeline/runMultiQC.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runMultiQC.sh -------------------------------------------------------------------------------- /pipeline/runMummer.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runMummer.sh -------------------------------------------------------------------------------- /pipeline/runMuscle.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runMuscle.sh -------------------------------------------------------------------------------- /pipeline/runNarromi.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runNarromi.sh -------------------------------------------------------------------------------- /pipeline/runNutil.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runNutil.sh -------------------------------------------------------------------------------- /pipeline/runOSA.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runOSA.sh -------------------------------------------------------------------------------- /pipeline/runPASA_GFF3_validator.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runPASA_GFF3_validator.sh -------------------------------------------------------------------------------- /pipeline/runPLEK.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runPLEK.sh -------------------------------------------------------------------------------- /pipeline/runPLncPRO.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runPLncPRO.sh -------------------------------------------------------------------------------- /pipeline/runParseMacs2.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runParseMacs2.sh -------------------------------------------------------------------------------- /pipeline/runPasaAlignment.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runPasaAlignment.sh -------------------------------------------------------------------------------- /pipeline/runPasaCompare.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runPasaCompare.sh -------------------------------------------------------------------------------- /pipeline/runPasaComprehensiveTranscriptomeBuilder.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runPasaComprehensiveTranscriptomeBuilder.sh -------------------------------------------------------------------------------- /pipeline/runPasaLoadAnnotation.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runPasaLoadAnnotation.sh -------------------------------------------------------------------------------- /pipeline/runPasaSeqclean.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runPasaSeqclean.sh -------------------------------------------------------------------------------- /pipeline/runPasaSupportingEvidenceAlignment.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runPasaSupportingEvidenceAlignment.sh -------------------------------------------------------------------------------- /pipeline/runPasaValidAnnotationUpdate.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runPasaValidAnnotationUpdate.sh -------------------------------------------------------------------------------- /pipeline/runPearsonSpearmanCorrelation.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runPearsonSpearmanCorrelation.sh -------------------------------------------------------------------------------- /pipeline/runPicardAddOrReplaceReadGroups.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runPicardAddOrReplaceReadGroups.sh -------------------------------------------------------------------------------- /pipeline/runPicardCreateSequenceDictionary.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runPicardCreateSequenceDictionary.sh -------------------------------------------------------------------------------- /pipeline/runPicardMarkDuplicatesWithMateCigar.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runPicardMarkDuplicatesWithMateCigar.sh -------------------------------------------------------------------------------- /pipeline/runPicardSamToFastq.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runPicardSamToFastq.sh -------------------------------------------------------------------------------- /pipeline/runPlaac.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runPlaac.sh -------------------------------------------------------------------------------- /pipeline/runPrepInfomap.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runPrepInfomap.sh -------------------------------------------------------------------------------- /pipeline/runProjectCreation.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runProjectCreation.sh -------------------------------------------------------------------------------- /pipeline/runProjectPermission.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runProjectPermission.sh -------------------------------------------------------------------------------- /pipeline/runProjectSetup.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runProjectSetup.sh -------------------------------------------------------------------------------- /pipeline/runPyfasta.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runPyfasta.sh -------------------------------------------------------------------------------- /pipeline/runPythonLncRNAFiltering.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runPythonLncRNAFiltering.py -------------------------------------------------------------------------------- /pipeline/runQCprot.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runQCprot.sh -------------------------------------------------------------------------------- /pipeline/runR.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runR.sh -------------------------------------------------------------------------------- /pipeline/runRNASeqGATKPreprocessing.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runRNASeqGATKPreprocessing.sh -------------------------------------------------------------------------------- /pipeline/runRNASeqPreprocessing.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runRNASeqPreprocessing.sh -------------------------------------------------------------------------------- /pipeline/runRNASeqSEPreprocessing.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runRNASeqSEPreprocessing.sh -------------------------------------------------------------------------------- /pipeline/runRePair.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runRePair.sh -------------------------------------------------------------------------------- /pipeline/runReaper.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runReaper.sh -------------------------------------------------------------------------------- /pipeline/runRemoveBlankLines.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runRemoveBlankLines.sh -------------------------------------------------------------------------------- /pipeline/runRepeatMasker.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runRepeatMasker.sh -------------------------------------------------------------------------------- /pipeline/runRepeatModeler.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runRepeatModeler.sh -------------------------------------------------------------------------------- /pipeline/runRiboSeqSePreprocessing.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runRiboSeqSePreprocessing.sh -------------------------------------------------------------------------------- /pipeline/runRmarkdown.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runRmarkdown.sh -------------------------------------------------------------------------------- /pipeline/runRnaSeqPipelineStats.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runRnaSeqPipelineStats.sh -------------------------------------------------------------------------------- /pipeline/runRscript.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runRscript.sh -------------------------------------------------------------------------------- /pipeline/runSRnaWorkBenchFilter.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSRnaWorkBenchFilter.sh -------------------------------------------------------------------------------- /pipeline/runSSPACE-LR.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSSPACE-LR.sh -------------------------------------------------------------------------------- /pipeline/runSTAR.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSTAR.sh -------------------------------------------------------------------------------- /pipeline/runSTARGenomeGenerate.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSTARGenomeGenerate.sh -------------------------------------------------------------------------------- /pipeline/runSTARGenomeLoad.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSTARGenomeLoad.sh -------------------------------------------------------------------------------- /pipeline/runSTARGenomeRemove.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSTARGenomeRemove.sh -------------------------------------------------------------------------------- /pipeline/runSTARStats.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSTARStats.sh -------------------------------------------------------------------------------- /pipeline/runSTAR_trx.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSTAR_trx.sh -------------------------------------------------------------------------------- /pipeline/runSUPPA2DiffSplice.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSUPPA2DiffSplice.sh -------------------------------------------------------------------------------- /pipeline/runSUPPA2GenerateEvents.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSUPPA2GenerateEvents.sh -------------------------------------------------------------------------------- /pipeline/runSUPPA2PsiPerEvent.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSUPPA2PsiPerEvent.sh -------------------------------------------------------------------------------- /pipeline/runSUPPA2PsiPerIsoform.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSUPPA2PsiPerIsoform.sh -------------------------------------------------------------------------------- /pipeline/runSalmon.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSalmon.py -------------------------------------------------------------------------------- /pipeline/runSalmon.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSalmon.sh -------------------------------------------------------------------------------- /pipeline/runSalmonIndex.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSalmonIndex.sh -------------------------------------------------------------------------------- /pipeline/runSalmonSE.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSalmonSE.sh -------------------------------------------------------------------------------- /pipeline/runSalmonStats.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSalmonStats.sh -------------------------------------------------------------------------------- /pipeline/runSampleN.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSampleN.sh -------------------------------------------------------------------------------- /pipeline/runSampleN_SE.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSampleN_SE.sh -------------------------------------------------------------------------------- /pipeline/runSamtoolsFaidx.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSamtoolsFaidx.sh -------------------------------------------------------------------------------- /pipeline/runSamtoolsFlagstat.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSamtoolsFlagstat.sh -------------------------------------------------------------------------------- /pipeline/runSamtoolsIdxstats.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSamtoolsIdxstats.sh -------------------------------------------------------------------------------- /pipeline/runSamtoolsIndex.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSamtoolsIndex.sh -------------------------------------------------------------------------------- /pipeline/runSamtoolsMerge.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSamtoolsMerge.sh -------------------------------------------------------------------------------- /pipeline/runSamtoolsReheader.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSamtoolsReheader.sh -------------------------------------------------------------------------------- /pipeline/runSamtoolsSort.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSamtoolsSort.sh -------------------------------------------------------------------------------- /pipeline/runSamtools_miRNAclusters.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSamtools_miRNAclusters.sh -------------------------------------------------------------------------------- /pipeline/runSamtools_split_primary.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSamtools_split_primary.sh -------------------------------------------------------------------------------- /pipeline/runSeidrAggregate.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSeidrAggregate.sh -------------------------------------------------------------------------------- /pipeline/runSeidrBackbone.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSeidrBackbone.sh -------------------------------------------------------------------------------- /pipeline/runSeidrRoc.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSeidrRoc.sh -------------------------------------------------------------------------------- /pipeline/runSeidrThreshold.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSeidrThreshold.sh -------------------------------------------------------------------------------- /pipeline/runShortstack.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runShortstack.sh -------------------------------------------------------------------------------- /pipeline/runSnpEff.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSnpEff.sh -------------------------------------------------------------------------------- /pipeline/runSnpEffBuild.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSnpEffBuild.sh -------------------------------------------------------------------------------- /pipeline/runSortmerna.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSortmerna.sh -------------------------------------------------------------------------------- /pipeline/runSortmernaDennis.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSortmernaDennis.sh -------------------------------------------------------------------------------- /pipeline/runSortmernaMtSSU.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSortmernaMtSSU.sh -------------------------------------------------------------------------------- /pipeline/runSortmernaStats.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSortmernaStats.sh -------------------------------------------------------------------------------- /pipeline/runSraFastqDump.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSraFastqDump.sh -------------------------------------------------------------------------------- /pipeline/runStarBamAndUnmappedToFastq.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runStarBamAndUnmappedToFastq.sh -------------------------------------------------------------------------------- /pipeline/runStarFusion.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runStarFusion.sh -------------------------------------------------------------------------------- /pipeline/runSwestoreSync.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runSwestoreSync.sh -------------------------------------------------------------------------------- /pipeline/runTIGLM.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runTIGLM.sh -------------------------------------------------------------------------------- /pipeline/runTaxonomicClassification.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runTaxonomicClassification.sh -------------------------------------------------------------------------------- /pipeline/runTaxonomyUpdate.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runTaxonomyUpdate.sh -------------------------------------------------------------------------------- /pipeline/runThresholdNetwork.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runThresholdNetwork.sh -------------------------------------------------------------------------------- /pipeline/runTransfer.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runTransfer.sh -------------------------------------------------------------------------------- /pipeline/runTremulaTranslate.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runTremulaTranslate.sh -------------------------------------------------------------------------------- /pipeline/runTrim.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runTrim.sh -------------------------------------------------------------------------------- /pipeline/runTrimmomatic.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runTrimmomatic.sh -------------------------------------------------------------------------------- /pipeline/runTrimmomaticSeStats.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runTrimmomaticSeStats.sh -------------------------------------------------------------------------------- /pipeline/runTrimmomaticStats.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runTrimmomaticStats.sh -------------------------------------------------------------------------------- /pipeline/runTrinity.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runTrinity.sh -------------------------------------------------------------------------------- /pipeline/runTrinityEstimateExpression.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runTrinityEstimateExpression.sh -------------------------------------------------------------------------------- /pipeline/runTrinityGenomeGuided.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runTrinityGenomeGuided.sh -------------------------------------------------------------------------------- /pipeline/runTrinitySE.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runTrinitySE.sh -------------------------------------------------------------------------------- /pipeline/runTrinityTransDecoder.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runTrinityTransDecoder.sh -------------------------------------------------------------------------------- /pipeline/runUpdateNCBI.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runUpdateNCBI.sh -------------------------------------------------------------------------------- /pipeline/runUsearch.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runUsearch.sh -------------------------------------------------------------------------------- /pipeline/runVCFPlot.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runVCFPlot.sh -------------------------------------------------------------------------------- /pipeline/runVCFStats.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runVCFStats.sh -------------------------------------------------------------------------------- /pipeline/runVsearch.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runVsearch.sh -------------------------------------------------------------------------------- /pipeline/runVsearchDatabase.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runVsearchDatabase.sh -------------------------------------------------------------------------------- /pipeline/runVsearchMergePairs.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runVsearchMergePairs.sh -------------------------------------------------------------------------------- /pipeline/runXxhashsum.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/runXxhashsum.sh -------------------------------------------------------------------------------- /pipeline/run_ClustalW.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/run_ClustalW.sh -------------------------------------------------------------------------------- /pipeline/run_HMMbuild.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/run_HMMbuild.sh -------------------------------------------------------------------------------- /pipeline/run_array_pseudopipe.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/run_array_pseudopipe.sh -------------------------------------------------------------------------------- /pipeline/run_array_repeatmasker.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/run_array_repeatmasker.sh -------------------------------------------------------------------------------- /pipeline/run_array_repeatmasker2.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/run_array_repeatmasker2.sh -------------------------------------------------------------------------------- /pipeline/run_array_repeatmasker2coredump.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/run_array_repeatmasker2coredump.sh -------------------------------------------------------------------------------- /pipeline/run_check_offtarget_for_guide_RNAs.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/run_check_offtarget_for_guide_RNAs.sh -------------------------------------------------------------------------------- /pipeline/run_makeblastdb_pglauca.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/run_makeblastdb_pglauca.sh -------------------------------------------------------------------------------- /pipeline/run_makeblastdb_ptaeda.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/run_makeblastdb_ptaeda.sh -------------------------------------------------------------------------------- /pipeline/run_ppfinder.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/run_ppfinder.sh -------------------------------------------------------------------------------- /pipeline/run_psari.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/run_psari.sh -------------------------------------------------------------------------------- /pipeline/run_pseudopipe.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/run_pseudopipe.sh -------------------------------------------------------------------------------- /pipeline/run_psf.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/run_psf.sh -------------------------------------------------------------------------------- /pipeline/sortMeRnaV2Stats.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/sortMeRnaV2Stats.sh -------------------------------------------------------------------------------- /pipeline/submit_nextflow_RNAseq.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/submit_nextflow_RNAseq.sh -------------------------------------------------------------------------------- /pipeline/the_master.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/the_master.sh -------------------------------------------------------------------------------- /pipeline/the_master_beta.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/the_master_beta.sh -------------------------------------------------------------------------------- /pipeline/the_master_v2.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/pipeline/the_master_v2.sh -------------------------------------------------------------------------------- /src/R/ARACNE.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/ARACNE.R -------------------------------------------------------------------------------- /src/R/GENIE3_simple.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/GENIE3_simple.R -------------------------------------------------------------------------------- /src/R/GeneNet.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/GeneNet.R -------------------------------------------------------------------------------- /src/R/Rmodules.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/Rmodules.R -------------------------------------------------------------------------------- /src/R/TIGLM.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/TIGLM.R -------------------------------------------------------------------------------- /src/R/TIGRESS.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/TIGRESS.R -------------------------------------------------------------------------------- /src/R/WgcnaClusterPlot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/WgcnaClusterPlot.R -------------------------------------------------------------------------------- /src/R/amplicon_basics.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/amplicon_basics.R -------------------------------------------------------------------------------- /src/R/blastUtilities.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/blastUtilities.R -------------------------------------------------------------------------------- /src/R/cigarUtility.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/cigarUtility.R -------------------------------------------------------------------------------- /src/R/convertTemplates.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/convertTemplates.R -------------------------------------------------------------------------------- /src/R/createGeneAnnotation.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/createGeneAnnotation.R -------------------------------------------------------------------------------- /src/R/createGeneModelGff.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/createGeneModelGff.R -------------------------------------------------------------------------------- /src/R/createMapFileForDeML.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/createMapFileForDeML.R -------------------------------------------------------------------------------- /src/R/createSyntheticTranscripts.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/createSyntheticTranscripts.R -------------------------------------------------------------------------------- /src/R/csawUtilities.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/csawUtilities.R -------------------------------------------------------------------------------- /src/R/densityPlot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/densityPlot.R -------------------------------------------------------------------------------- /src/R/deviseSequenceFromGFF.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/deviseSequenceFromGFF.R -------------------------------------------------------------------------------- /src/R/enaCsvEdit.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/enaCsvEdit.R -------------------------------------------------------------------------------- /src/R/expressionSpecificityUtility.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/expressionSpecificityUtility.R -------------------------------------------------------------------------------- /src/R/expressionSpecificityUtility.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/expressionSpecificityUtility.html -------------------------------------------------------------------------------- /src/R/extractGff3Subset.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/extractGff3Subset.R -------------------------------------------------------------------------------- /src/R/extractPromoter_Template_.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/extractPromoter_Template_.R -------------------------------------------------------------------------------- /src/R/featureSelection.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/featureSelection.R -------------------------------------------------------------------------------- /src/R/featureSelection.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/featureSelection.html -------------------------------------------------------------------------------- /src/R/functions_DifferentialExpression.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/functions_DifferentialExpression.R -------------------------------------------------------------------------------- /src/R/functions_GOenrichment_TopGO.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/functions_GOenrichment_TopGO.R -------------------------------------------------------------------------------- /src/R/functions_ancombc.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/functions_ancombc.R -------------------------------------------------------------------------------- /src/R/genericRnaSeq.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/genericRnaSeq.R -------------------------------------------------------------------------------- /src/R/genericRnaSeq.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/genericRnaSeq.html -------------------------------------------------------------------------------- /src/R/getCoverage.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/getCoverage.R -------------------------------------------------------------------------------- /src/R/gff3Utilities.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/gff3Utilities.R -------------------------------------------------------------------------------- /src/R/gff3Utilities.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/gff3Utilities.html -------------------------------------------------------------------------------- /src/R/ggComparisonplot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/ggComparisonplot.R -------------------------------------------------------------------------------- /src/R/gmapUtilities.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/gmapUtilities.R -------------------------------------------------------------------------------- /src/R/gopher.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/gopher.R -------------------------------------------------------------------------------- /src/R/gopher2-example.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/gopher2-example.R -------------------------------------------------------------------------------- /src/R/mailR.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/mailR.R -------------------------------------------------------------------------------- /src/R/metageneUtilities.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/metageneUtilities.R -------------------------------------------------------------------------------- /src/R/methylKitPCA_withVar.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/methylKitPCA_withVar.R -------------------------------------------------------------------------------- /src/R/methylation_utils.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/methylation_utils.R -------------------------------------------------------------------------------- /src/R/misoPePlot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/misoPePlot.R -------------------------------------------------------------------------------- /src/R/parseUniRef90IDs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/parseUniRef90IDs.R -------------------------------------------------------------------------------- /src/R/parse_gmap.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/parse_gmap.R -------------------------------------------------------------------------------- /src/R/pasaUtilities.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/pasaUtilities.R -------------------------------------------------------------------------------- /src/R/pasaUtilities.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/pasaUtilities.html -------------------------------------------------------------------------------- /src/R/percentile.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/percentile.R -------------------------------------------------------------------------------- /src/R/pfamUtilities.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/pfamUtilities.R -------------------------------------------------------------------------------- /src/R/plot.alphabetByCycle.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/plot.alphabetByCycle.R -------------------------------------------------------------------------------- /src/R/plot.multidensity.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/plot.multidensity.R -------------------------------------------------------------------------------- /src/R/plotClusterNetwork.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/plotClusterNetwork.R -------------------------------------------------------------------------------- /src/R/plotDispLSD.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/plotDispLSD.R -------------------------------------------------------------------------------- /src/R/plotEnrichedTreemap.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/plotEnrichedTreemap.R -------------------------------------------------------------------------------- /src/R/plotMA.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/plotMA.R -------------------------------------------------------------------------------- /src/R/plotSft.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/plotSft.R -------------------------------------------------------------------------------- /src/R/plotVCFQual.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/plotVCFQual.R -------------------------------------------------------------------------------- /src/R/plotVennDiagram.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/plotVennDiagram.R -------------------------------------------------------------------------------- /src/R/pseudoChromosomeUtilities.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/pseudoChromosomeUtilities.R -------------------------------------------------------------------------------- /src/R/rePairFastq.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/rePairFastq.R -------------------------------------------------------------------------------- /src/R/reverseFastq.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/reverseFastq.R -------------------------------------------------------------------------------- /src/R/rfam5SKrakenPrep.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/rfam5SKrakenPrep.R -------------------------------------------------------------------------------- /src/R/rmd.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/rmd.R -------------------------------------------------------------------------------- /src/R/salmonPEplusSE.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/salmonPEplusSE.R -------------------------------------------------------------------------------- /src/R/salmonPEplusSE.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/salmonPEplusSE.html -------------------------------------------------------------------------------- /src/R/salmonUtilities.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/salmonUtilities.R -------------------------------------------------------------------------------- /src/R/sequenceUtilities.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/sequenceUtilities.R -------------------------------------------------------------------------------- /src/R/sequenceUtilities.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/sequenceUtilities.html -------------------------------------------------------------------------------- /src/R/topGoUtilities.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/topGoUtilities.R -------------------------------------------------------------------------------- /src/R/topGoUtilities.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/topGoUtilities.html -------------------------------------------------------------------------------- /src/R/try opt.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/try opt.R -------------------------------------------------------------------------------- /src/R/updateAspenVcfv1.0.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/updateAspenVcfv1.0.R -------------------------------------------------------------------------------- /src/R/updateTaxonomyDivisionTable.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/updateTaxonomyDivisionTable.R -------------------------------------------------------------------------------- /src/R/volcanoPlot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/R/volcanoPlot.R -------------------------------------------------------------------------------- /src/bash/23s_silva_installation.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/bash/23s_silva_installation.sh -------------------------------------------------------------------------------- /src/bash/5S_rfam_installation.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/bash/5S_rfam_installation.sh -------------------------------------------------------------------------------- /src/bash/functions.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/bash/functions.sh -------------------------------------------------------------------------------- /src/bash/oneliners.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/bash/oneliners.md -------------------------------------------------------------------------------- /src/bash/seidr-aggregate-kebnekaise.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/bash/seidr-aggregate-kebnekaise.sh -------------------------------------------------------------------------------- /src/bash/seidr-aracne.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/bash/seidr-aracne.sh -------------------------------------------------------------------------------- /src/bash/seidr-elnet-wrapper-kebnekaise.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/bash/seidr-elnet-wrapper-kebnekaise.sh -------------------------------------------------------------------------------- /src/bash/seidr-elnet-wrapper.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/bash/seidr-elnet-wrapper.sh -------------------------------------------------------------------------------- /src/bash/seidr-import-kebnekaise.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/bash/seidr-import-kebnekaise.sh -------------------------------------------------------------------------------- /src/bash/seidr-import-micro.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/bash/seidr-import-micro.sh -------------------------------------------------------------------------------- /src/bash/seidr-wrapper-kebnekaise.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/bash/seidr-wrapper-kebnekaise.sh -------------------------------------------------------------------------------- /src/bash/seidr-wrapper-micro.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/bash/seidr-wrapper-micro.sh -------------------------------------------------------------------------------- /src/bash/try-catch-example.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/bash/try-catch-example.sh -------------------------------------------------------------------------------- /src/bash/try-catch.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/bash/try-catch.sh -------------------------------------------------------------------------------- /src/bash/updateTaxonomySqlite.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/bash/updateTaxonomySqlite.sh -------------------------------------------------------------------------------- /src/python/fastQCmultiviewer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/python/fastQCmultiviewer.py -------------------------------------------------------------------------------- /src/python/generate_import_script.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/src/python/generate_import_script.py -------------------------------------------------------------------------------- /templates/R/BiologicalQA.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/templates/R/BiologicalQA.R -------------------------------------------------------------------------------- /templates/R/BiologicalQA.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/templates/R/BiologicalQA.Rmd -------------------------------------------------------------------------------- /templates/R/DE_template.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/templates/R/DE_template.Rmd -------------------------------------------------------------------------------- /templates/R/DifferentialAbundance_ANCOMBC2_tentative.qmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/templates/R/DifferentialAbundance_ANCOMBC2_tentative.qmd -------------------------------------------------------------------------------- /templates/R/DifferentialExpression.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/templates/R/DifferentialExpression.R -------------------------------------------------------------------------------- /templates/R/DifferentialExpression_WithGOenrichment.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/templates/R/DifferentialExpression_WithGOenrichment.Rmd -------------------------------------------------------------------------------- /templates/R/Mfuzz.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/templates/R/Mfuzz.R -------------------------------------------------------------------------------- /templates/R/Network_Clustering_with_Leiden.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/templates/R/Network_Clustering_with_Leiden.R -------------------------------------------------------------------------------- /templates/R/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/templates/R/README.md -------------------------------------------------------------------------------- /templates/R/WorkInProgress_DifferentialExpression_WithAllEnrichment.qmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/templates/R/WorkInProgress_DifferentialExpression_WithAllEnrichment.qmd -------------------------------------------------------------------------------- /templates/R/bulogo2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/templates/R/bulogo2.png -------------------------------------------------------------------------------- /templates/R/empty.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/templates/R/empty.R -------------------------------------------------------------------------------- /templates/R/footer.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/templates/R/footer.html -------------------------------------------------------------------------------- /templates/R/header.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/templates/R/header.html -------------------------------------------------------------------------------- /templates/R/seidrFirstDegreeNeighbour.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/templates/R/seidrFirstDegreeNeighbour.R -------------------------------------------------------------------------------- /templates/R/seidrPageRank.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/templates/R/seidrPageRank.R -------------------------------------------------------------------------------- /templates/R/seidrPreparation.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/templates/R/seidrPreparation.R -------------------------------------------------------------------------------- /templates/R/seidrRoc.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/templates/R/seidrRoc.R -------------------------------------------------------------------------------- /templates/R/style.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/templates/R/style.css -------------------------------------------------------------------------------- /templates/bash/cleanup.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/templates/bash/cleanup.sh -------------------------------------------------------------------------------- /templates/bash/runTemplate.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/templates/bash/runTemplate.sh -------------------------------------------------------------------------------- /templates/bash/submitSeidrAggregate.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/templates/bash/submitSeidrAggregate.sh -------------------------------------------------------------------------------- /templates/bash/submitSeidrBackbone.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/templates/bash/submitSeidrBackbone.sh -------------------------------------------------------------------------------- /templates/bash/submitSeidrRoc.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/templates/bash/submitSeidrRoc.sh -------------------------------------------------------------------------------- /templates/bash/template.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/templates/bash/template.sh -------------------------------------------------------------------------------- /templates/python/Network_Clustering_with_Leiden.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UPSCb/UPSCb-common/HEAD/templates/python/Network_Clustering_with_Leiden.py --------------------------------------------------------------------------------