├── .github ├── styler.R └── workflows │ ├── ci.yaml │ ├── pr.yaml │ └── slash.yaml ├── .gitignore ├── .gitmodules ├── .tt_biocontainer_skip ├── .tt_skip ├── LICENSE ├── README.md ├── deprecated └── tools │ ├── MultiPEN │ ├── MultiPEN-StringDBNetwork.xml │ ├── MultiPEN-cross-validation.xml │ ├── MultiPEN-enrichment-GO.xml │ ├── MultiPEN-enrichment-KEGG.xml │ ├── MultiPEN-feature-selection.xml │ └── test-data │ │ ├── MultiPEN-Rankings_lambda0.0001-onlyGenes.txt │ │ ├── MultiPEN-Rankings_lambda0.0001.txt │ │ ├── MultiPEN-Rankings_lambda0.0001_higher-in-cases.txt │ │ ├── MultiPEN-Rankings_lambda0.0001_higher-in-control.txt │ │ ├── MultiPEN-feature-selection_config.txt │ │ ├── MultiPEN-performance_feature-selection_lambda0.0001.txt │ │ ├── MultiPEN-vts_lambda0.0001.txt │ │ ├── cross-validation_stats.txt │ │ ├── edges-for-cross-validation.txt │ │ ├── enrichment-GO.txt │ │ ├── enrichment-GO_BP.pdf │ │ ├── enrichment-GO_CC.pdf │ │ ├── enrichment-GO_MF.pdf │ │ ├── expressionData.txt │ │ ├── geneList.txt │ │ ├── groups.txt │ │ ├── gse-GO.txt │ │ ├── gse-KEGG.txt │ │ ├── interactionMatrix.txt │ │ ├── networkFromGeneList.txt │ │ └── sampleClass.txt │ ├── ensembl_longest_cds_per_gene │ ├── .shed.yml │ ├── ensembl_longest_cds_per_gene.py │ ├── ensembl_longest_cds_per_gene.xml │ └── test-data │ │ ├── Mus_musculus.GRCm38.cds.first100.fa │ │ └── Mus_musculus.GRCm38.cds.longest.fa │ ├── rsat_filter_snps │ ├── .lint_skip │ ├── .shed.yml │ ├── rsat_filter_snps.py │ ├── rsat_filter_snps.xml │ └── test-data │ │ ├── rsat_filter_snps_out.tabular │ │ ├── rsat_output.tabular │ │ └── snp_positions.tabular │ └── targetscan │ ├── targetscan.xml │ └── test-data │ ├── All_cell_lines.AIRs.txt │ ├── ORF_8mer_counts_sample.txt │ ├── ORF_Sequences_sample.txt │ ├── Targets.BL_PCT.context_scores.txt │ ├── UTR_Sequences_sample.txt │ ├── UTRs_median_BLs_bins.txt │ ├── miR_Family_info_sample.txt │ ├── miR_for_context_scores.sample.txt │ ├── targetscan_70_output.BL_PCT.txt │ └── targetscan_70_output.txt ├── docker └── GSTF-docker │ ├── Dockerfile │ ├── library_data.yml │ ├── readme.md │ ├── tools.yml │ └── workflow │ └── gstf.ga ├── setup.cfg ├── tools ├── Ensembl-REST │ ├── .shed.yml │ ├── get_feature_info.py │ ├── get_feature_info.xml │ ├── get_genetree.py │ ├── get_genetree.xml │ ├── get_sequences.py │ ├── get_sequences.xml │ ├── macros.xml │ └── test-data │ │ └── input.txt ├── GAFA │ ├── .shed.yml │ ├── GAFA.py │ ├── GAFA.xml │ ├── schema │ │ ├── gafa.mwb │ │ ├── gafa.png │ │ ├── gafa.sql │ │ └── gafa.svg │ └── test-data │ │ ├── align1.fasta │ │ ├── align2.fasta │ │ ├── align3.fasta │ │ ├── align4.fasta │ │ ├── gene.sqlite │ │ ├── test.gafa.sqlite │ │ ├── tree1.nhx │ │ ├── tree2.nhx │ │ ├── tree3.nhx │ │ └── tree4.nhx ├── TreeBest │ ├── .shed.yml │ ├── TreeBest_best.xml │ └── test-data │ │ ├── dna_alignment.fasta │ │ ├── genetree.nhx │ │ └── species.nhx ├── apoc │ ├── .shed.yml │ ├── apoc.xml │ └── test-data │ │ └── apoc │ │ ├── 1ha3A.pdb │ │ ├── 1yr8A.pdb │ │ ├── 3ec1A.pdb │ │ ├── query.lst │ │ └── templ.lst ├── blast_parser │ ├── .shed.yml │ ├── blast_parser.py │ ├── blast_parser.xml │ └── test-data │ │ ├── input.tabular │ │ ├── output.tabular │ │ └── output2.tabular ├── ete │ ├── .shed.yml │ ├── ete_gene_cnv.py │ ├── ete_gene_cnv.xml │ ├── ete_genetree_splitter.py │ ├── ete_genetree_splitter.xml │ ├── ete_homology_classifier.py │ ├── ete_homology_classifier.xml │ ├── ete_init_taxdb.py │ ├── ete_init_taxdb.xml │ ├── ete_lineage_generator.py │ ├── ete_lineage_generator.xml │ ├── ete_macros.xml │ ├── ete_mod.xml │ ├── ete_species_tree_generator.py │ ├── ete_species_tree_generator.xml │ └── test-data │ │ ├── 11_genetree.nhx │ │ ├── 11_homology.csv │ │ ├── 11_homology.tabular │ │ ├── 12_genetree.nhx │ │ ├── 13_genetree.nhx │ │ ├── 14_genetree.nhx │ │ ├── 21_genetree.nhx │ │ ├── 22_genetree.nhx │ │ ├── 23_genetree.nhx │ │ ├── 24_genetree.nhx │ │ ├── 25_genetree.nhx │ │ ├── 31_genetree.nhx │ │ ├── 32_genetree.nhx │ │ ├── 33_genetree.nhx │ │ ├── 34_genetree.nhx │ │ ├── 41_genetree.nhx │ │ ├── 42_genetree.nhx │ │ ├── 43_genetree.nhx │ │ ├── 44_genetree.nhx │ │ ├── genetree.nhx │ │ ├── lineage-compress-lower.txt │ │ ├── lineage-compress.txt │ │ ├── lineage-full.txt │ │ ├── lineage-wid.txt │ │ ├── lineage.txt │ │ ├── species.txt │ │ ├── species_ids.txt │ │ ├── speciestree.nhx │ │ ├── taxdump.sqlite │ │ ├── taxdump.tar.gz │ │ ├── test.nhx │ │ ├── test.tsv │ │ ├── tree1.nhx │ │ ├── tree1_ladder.nhx │ │ ├── tree1_ogA.nhx │ │ ├── tree1_pruneAC.nhx │ │ ├── tree1_pruneACpreserve.nhx │ │ ├── tree1_unroot.nhx │ │ ├── tree1_unroot_resolve.nhx │ │ ├── tree2.nhx │ │ ├── tree2_sort.nhx │ │ ├── tree3.nhx │ │ └── tree3_stand.nhx ├── export_to_cluster │ ├── .lint_skip │ ├── .shed.yml │ ├── README.rst │ ├── export_to_cluster.py │ ├── export_to_cluster.xml │ └── tool_dependencies.xml ├── gblocks │ ├── .shed.yml │ ├── gblocks.xml │ └── test-data │ │ ├── Gblocks_Results_And_Parameters_on_data_95_html.html │ │ ├── Gblocks_Selected_Blocks_on_data_95.txt │ │ ├── Gblocks_on_data_95.txt │ │ └── nad3.fasta ├── gstf_preparation │ ├── .shed.yml │ ├── gstf_preparation.py │ ├── gstf_preparation.xml │ ├── schema │ │ ├── gstf.mwb │ │ ├── gstf.png │ │ └── gstf.svg │ └── test-data │ │ ├── CDS.fasta │ │ ├── Caenorhabditis_elegans.WBcel235.87.chromosome.I.shortened.gff3 │ │ ├── Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa │ │ ├── MGP_PahariEiJ_G0008413.1.gff3 │ │ ├── Mus_pahari.PAHARI_EIJ_v1.1.cds.all.shortened.fa │ │ ├── gene.json │ │ ├── test1.fasta │ │ ├── test1.sqlite │ │ ├── test1_longest.fasta │ │ ├── test4.fasta │ │ ├── test4.sqlite │ │ ├── test5.ns.fasta │ │ ├── test5_filtered.fasta │ │ ├── test6.fasta │ │ └── test6.sqlite ├── hcluster_sg │ ├── .shed.yml │ ├── hcluster_sg.xml │ └── test-data │ │ ├── exam-1.txt │ │ ├── hcluster_sg1.txt │ │ └── hcluster_sg2.txt ├── hcluster_sg_parser │ ├── .shed.yml │ ├── hcluster_sg_parser.py │ ├── hcluster_sg_parser.xml │ └── test-data │ │ ├── 0_output.txt │ │ ├── 1_output.txt │ │ ├── 2_output.txt │ │ ├── 3_output.txt │ │ ├── discarded.txt │ │ ├── empty.txt │ │ ├── hcluster_sg.tabular │ │ ├── hcluster_sg1.tabular │ │ ├── hcluster_sg1_0_output.txt │ │ ├── hcluster_sg1_1_output.txt │ │ ├── hcluster_sg1_2_output.txt │ │ ├── hcluster_sg1_3_output.txt │ │ ├── hcluster_sg1_4_output.txt │ │ ├── hcluster_sg1_5_output.txt │ │ ├── hcluster_sg1_6_output.txt │ │ ├── hcluster_sg1_7_output.txt │ │ └── hcluster_sg1_8_output.txt ├── lotus2 │ ├── .shed.yml │ ├── lotus2.xml │ ├── test-data │ │ ├── Anh_sample1.fastq.gz │ │ ├── Anh_sample2.fastq.gz │ │ ├── Arabidopsis_R1.fastqsanger.gz │ │ ├── Arabidopsis_R2.fastqsanger.gz │ │ ├── OTU.fna │ │ ├── OTU.txt │ │ ├── OTU_paired.fna │ │ ├── OTU_paired.txt │ │ ├── mapping.txt │ │ └── mapping_paired.txt │ ├── tool-data │ │ └── all_fasta.loc.sample │ └── tool_data_table_conf.xml.sample ├── miranda │ ├── .shed.yml │ ├── miranda.xml │ ├── miranda_parser.py │ └── test-data │ │ ├── microrna.fasta │ │ ├── query.fasta │ │ ├── raw_output.txt │ │ └── tabular_output.txt ├── plotheatmap │ ├── .lint_skip │ ├── .shed.yml │ ├── plotheatmap.xml │ ├── script.R │ └── test-data │ │ ├── count.matrix │ │ ├── heatmap.pdf │ │ └── stats.data ├── rdock │ ├── .shed.yml │ ├── rdock.xml │ └── test-data │ │ ├── 1sj0_ligand.sd │ │ ├── 1sj0_rdock.mol2 │ │ └── 1sj0_rdock.prm ├── replace_chromosome_names │ ├── .lint_skip │ ├── .shed.yml │ ├── replace_chromosome_names.py │ ├── replace_chromosome_names.xml │ └── test-data │ │ ├── GRCh37_ensembl2UCSC.txt │ │ ├── gemini_load_input.vcf │ │ └── replace_chromosome_names_output.vcf ├── smart_domains │ ├── .shed.yml │ ├── smart-domain.pl │ ├── smart_domains.xml │ └── test-data │ │ ├── ENSCAFP00000021307_SMART_results.json │ │ ├── ENSCAFP00000021307_SMART_results.txt │ │ ├── ENSCAFP00000021330_SMART_results.json │ │ ├── ENSCAFP00000021330_SMART_results.txt │ │ ├── ENSMUSP00000026013_SMART_results.json │ │ ├── ENSMUSP00000026013_SMART_results.txt │ │ ├── ENSMUSP00000040550_SMART_results.json │ │ ├── ENSMUSP00000040550_SMART_results.txt │ │ ├── ENSP00000340684_SMART_results.json │ │ ├── ENSP00000340684_SMART_results.txt │ │ ├── ENSP00000367309_SMART_results.json │ │ ├── ENSP00000367309_SMART_results.txt │ │ ├── ENSPTRP00000037440_SMART_results.json │ │ ├── ENSPTRP00000037440_SMART_results.txt │ │ ├── ENSPTRP00000037441_SMART_results.json │ │ ├── ENSPTRP00000037441_SMART_results.txt │ │ ├── ENSRNOP00000043466_SMART_results.json │ │ ├── ENSRNOP00000043466_SMART_results.txt │ │ ├── ENSRNOP00000063784_SMART_results.json │ │ ├── ENSRNOP00000063784_SMART_results.txt │ │ ├── ENSSSCP00000013044_SMART_results.json │ │ ├── ENSSSCP00000013044_SMART_results.txt │ │ ├── ENSSSCP00000028353_SMART_results.json │ │ ├── ENSSSCP00000028353_SMART_results.txt │ │ └── seq.fa ├── smina │ ├── .shed.yml │ ├── smina.xml │ └── test-data │ │ ├── ligand.pdbqt │ │ ├── ligand_out.pdbqt │ │ ├── output_smina │ │ └── protein.pdbqt └── t_coffee │ ├── .shed.yml │ ├── filter_by_fasta_ids.py │ ├── t_coffee.xml │ └── test-data │ ├── ids.txt │ ├── input.fasta │ ├── output1.fasta │ ├── output2.fasta │ ├── output3.fasta_seq │ ├── output3.nhx │ └── output3.pir_seq ├── visualisations └── aequatus │ ├── README.md │ ├── config │ └── aequatus.xml │ ├── static │ ├── aequatus.css │ ├── controls.js │ ├── popup.js │ ├── scriptaculous │ │ └── prototype.js │ ├── scripts │ │ ├── controls.js │ │ ├── popup.js │ │ ├── readSQLite.js │ │ ├── sql.js │ │ ├── worker.js │ │ └── worker.sql.js │ └── styles │ │ └── aequatus.css │ └── templates │ └── aequatus.mako └── workflows └── GeneSeqToFamily ├── .shed.yml ├── GeneFamilies_GeneSeqToFamily.ga ├── GeneSeqToFamily.ga ├── GeneSeqToFamily.png ├── finding_orphan_genes.ga ├── finding_orphan_genes.png ├── readme.md ├── swissprot.ga ├── swissprot.png ├── test-data ├── CDS.fasta ├── gene.json ├── gene_family.gafa.sqlite └── species.nhx └── tutorial.md /.github/styler.R: -------------------------------------------------------------------------------- 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