├── .gitignore ├── README.md ├── apps ├── DscCR │ ├── DESCRIPTION │ ├── DscCR.Rproj │ ├── NAMESPACE │ ├── R │ │ ├── dscc.R │ │ ├── tbd.R │ │ └── zzz.R │ ├── src │ │ ├── DscCR.so │ │ ├── Makevars │ │ ├── c_threads.c │ │ ├── c_threads.h │ │ ├── c_threads.o │ │ ├── compute.c │ │ ├── compute.h │ │ ├── compute.o │ │ ├── dscc.c │ │ ├── dscc.o │ │ ├── perm.c │ │ ├── perm.h │ │ └── perm.o │ └── tests │ │ ├── compare_dsc_times.R │ │ └── dsc_c_test.R ├── MBatch │ ├── .Renviron │ ├── DESCRIPTION │ ├── MBatch.Rproj │ ├── Meta │ │ └── vignette.rds │ ├── NAMESPACE │ ├── NEWS │ ├── R │ │ ├── ALL_BEA_objects.R │ │ ├── BEA_Assessments.R │ │ ├── BEA_AssessmentsAPI.R │ │ ├── BEA_AssessmentsBatchcorr.R │ │ ├── BEA_AssessmentsBoxplot.R │ │ ├── BEA_AssessmentsCDP.R │ │ ├── BEA_AssessmentsHierclust.R │ │ ├── BEA_AssessmentsPca.R │ │ ├── BEA_AssessmentsPca_dsc.R │ │ ├── BEA_AssessmentsPca_pvalueDsc.R │ │ ├── BEA_AssessmentsSupervisedClust.R │ │ ├── BEA_AssessmentsUmap.R │ │ ├── BEA_AssessmentsVolcano.R │ │ ├── BEA_CorrectionsAN.R │ │ ├── BEA_CorrectionsAPI.R │ │ ├── BEA_CorrectionsEB.R │ │ ├── BEA_CorrectionsEBNP.R │ │ ├── BEA_CorrectionsEBNPapi.R │ │ ├── BEA_CorrectionsEBNPdata.R │ │ ├── BEA_CorrectionsEBNplus.R │ │ ├── BEA_CorrectionsMP.R │ │ ├── BEA_CorrectionsRBN.R │ │ ├── BEA_CorrectionsRBNapi.R │ │ ├── BEA_DapiQuery.R │ │ ├── BEA_SeuratObj.R │ │ ├── BatchEffAssess.R │ │ ├── FilesAndDirs.R │ │ ├── InternalVariables.R │ │ ├── Logging.R │ │ └── zzz.R │ ├── README.md │ ├── doc │ │ ├── MBatch_04-06_PCA_DualBatch_Structures.pdf │ │ ├── MBatch_04-07_SupervisedClustering_Pairs_Structures.pdf │ │ ├── MBatch_04-08_Boxplot_AllSamplesRLE_Structures.pdf │ │ ├── MBatch_04-09_Boxplot_AllSamplesData_Structures.pdf │ │ ├── MBatch_05-05_EB_withNonParametricPriors.pdf │ │ ├── MBatch_05-06_EB_withParametricPriors.pdf │ │ ├── MBatch_05-07_MP_Overall.pdf │ │ ├── MBatch_05-08_MP_ByBatch.pdf │ │ ├── MBatch_05-09_AN_Adjusted.pdf │ │ ├── MBatch_05-10_AN_Unadjusted.pdf │ │ ├── MBatch_05-11_EBNPlus_CheckData_Structures.pdf │ │ ├── MBatch_05-12_EBNPlus_TrainAndValidateReplicates_Structures.pdf │ │ └── MBatch_05-13_EBNPlus_TrainAndValidateFromVector_Structures.pdf │ ├── inst │ │ └── gpl-2_0.txt │ ├── installing.txt │ ├── java │ │ └── README.txt │ ├── man │ │ ├── AN_Adjusted.Rd │ │ ├── AN_Unadjusted.Rd │ │ ├── BEA_DATA-class.Rd │ │ ├── Boxplot_AllSamplesData_Structures.Rd │ │ ├── Boxplot_AllSamplesRLE_Structures.Rd │ │ ├── Boxplot_Group_Structures.Rd │ │ ├── CDP_Files.Rd │ │ ├── CDP_Plot.Rd │ │ ├── CDP_Structures.Rd │ │ ├── EBNPlus_CheckData_Structures.Rd │ │ ├── EBNPlus_CombineBatches.Rd │ │ ├── EBNPlus_Correction_Files.Rd │ │ ├── EBNPlus_Correction_Structures.Rd │ │ ├── EBNPlus_TrainAndValidateFromVector_Structures.Rd │ │ ├── EBNPlus_TrainAndValidateReplicates_Structures.Rd │ │ ├── EB_withNonParametricPriors.Rd │ │ ├── EB_withParametricPriors.Rd │ │ ├── HierarchicalClustering_Structures.Rd │ │ ├── Logging-class.Rd │ │ ├── MP_ByBatch.Rd │ │ ├── MP_Overall.Rd │ │ ├── PCA_DualBatch_Structures.Rd │ │ ├── PCA_Regular_Structures.Rd │ │ ├── RBN_Pseudoreplicates.Rd │ │ ├── RBN_Replicates.Rd │ │ ├── SupervisedClustering_Batches_Structures.Rd │ │ ├── SupervisedClustering_Pairs_Structures.Rd │ │ ├── UMAP_Structures.Rd │ │ ├── buildDSCOverviewFile.Rd │ │ ├── clearDSCOverviewFiles.Rd │ │ ├── convertSeuratObjtoStdDataObj.Rd │ │ ├── convertSeuratRDStoStdDataFiles.Rd │ │ ├── downloadDataBatches.Rd │ │ ├── downloadDataMatrix.Rd │ │ ├── downloadNgchmHtml.Rd │ │ ├── downloadNgchmNgchm.Rd │ │ ├── getDapiQuery.Rd │ │ ├── getDownloadableForDataset.Rd │ │ ├── getGlobalMBatchEnv.Rd │ │ ├── getReplicatesForRBN.Rd │ │ ├── mbatchFilterData.Rd │ │ ├── mbatchIncludeExcludeData.Rd │ │ ├── mbatchLoadFiles.Rd │ │ ├── mbatchLoadStructures.Rd │ │ ├── mbatchTrimData.Rd │ │ ├── mbatchWriteSuccessfulLog.Rd │ │ ├── readAsGenericDataframe.Rd │ │ ├── readAsGenericMatrix.Rd │ │ ├── setGlobalMBatchEnv.Rd │ │ ├── setLogging.Rd │ │ ├── updateDapiQuery.Rd │ │ ├── updateOrBuildSeuratObjectFromStdDataFiles.Rd │ │ ├── updateOrBuildSeuratObjectFromStdDataObjs.Rd │ │ ├── writeAsGenericDataframe.Rd │ │ └── writeAsGenericMatrix.Rd │ ├── tests │ │ ├── AN_Adjusted.R │ │ ├── AN_Unadjusted.R │ │ ├── Boxplot_AllSamplesData_Structures.R │ │ ├── Boxplot_AllSamplesRLE_Structures.R │ │ ├── Boxplot_Group_Structures.R │ │ ├── CDP_Files.R │ │ ├── CDP_Plot.R │ │ ├── CDP_Structures.R │ │ ├── DapiQuery_download.R │ │ ├── EBNPlus_CombineBatches.R │ │ ├── EBNPlus_Correction_Files.R │ │ ├── EBNPlus_Correction_Structures.R │ │ ├── EBNPlus_TrainAndValidate.R │ │ ├── EB_withNonParametricPriors.R │ │ ├── EB_withParametricPriors.R │ │ ├── HierarchicalClustering_Structures.R │ │ ├── MP_ByBatch.R │ │ ├── MP_Overall.R │ │ ├── MWB_UMAP_Structures.R │ │ ├── PCA_DualBatch_Structures.R │ │ ├── PCA_Regular_Structures.R │ │ ├── RBN_Pseudoreplicates.R │ │ ├── RBN_Replicates.R │ │ ├── SeuratObj_rds.R │ │ ├── SeuratObj_std.R │ │ ├── SupervisedClustering_Batches_Structures.R │ │ ├── SupervisedClustering_Pairs_Structures.R │ │ ├── UMAP_Structures.R │ │ ├── Volcano_Structures.R │ │ └── configLength.R │ └── vignettes │ │ ├── BoxPlot_AllSample-Data_Diagram-TSS.png │ │ ├── BoxPlot_AllSample-RLE_Diagram-BatchId.png │ │ ├── MBatch_04-06_PCA_DualBatch_Structures.Rmd │ │ ├── MBatch_04-07_SupervisedClustering_Pairs_Structures.Rmd │ │ ├── MBatch_04-08_Boxplot_AllSamplesRLE_Structures.Rmd │ │ ├── MBatch_04-09_Boxplot_AllSamplesData_Structures.Rmd │ │ ├── MBatch_04-10_HierarchicalClustering.Rmd │ │ ├── MBatch_05-05_EB_withNonParametricPriors.Rmd │ │ ├── MBatch_05-06_EB_withParametricPriors.Rmd │ │ ├── MBatch_05-07_MP_Overall.Rmd │ │ ├── MBatch_05-08_MP_ByBatch.Rmd │ │ ├── MBatch_05-09_AN_Adjusted.Rmd │ │ ├── MBatch_05-10_AN_Unadjusted.Rmd │ │ ├── MBatch_05-11_EBNPlus_CheckData_Structures.Rmd │ │ ├── MBatch_05-12_EBNPlus_TrainAndValidateReplicates_Structures.Rmd │ │ ├── MBatch_05-13_EBNPlus_TrainAndValidateFromVector_Structures.Rmd │ │ ├── boxplot_dynamic.PNG │ │ ├── boxplot_dynamic_data.PNG │ │ ├── pca_plus.png │ │ └── supervised_clustering.png ├── MBatchUtils │ ├── .Renviron │ ├── DESCRIPTION │ ├── MBatchUtils.Rproj │ ├── NAMESPACE │ ├── NEWS │ ├── R │ │ ├── BatchHeatMap.R │ │ ├── GSColors.R │ │ ├── MBatchUtils.R │ │ ├── MatrixBatchAssessAPI.R │ │ ├── MutationBatchAssessAPI.R │ │ ├── MutationBatchExtractAPI.R │ │ ├── MutationBatchReport.R │ │ ├── buildArchive.R │ │ ├── runFromConfig.R │ │ ├── runRBNfromConfig.R │ │ ├── test_mbatch_assessments.R │ │ └── zzz.R │ ├── doc │ │ └── MBatchUtils_MakeZipArchive.pdf │ ├── inst │ │ ├── BEVIndex │ │ │ ├── tooltip_gdc.tsv │ │ │ └── tooltip_tcga.tsv │ │ └── gpl-2_0.txt │ ├── man │ │ ├── buildBatchHeatMap_Files.Rd │ │ ├── buildBatchHeatMap_Structures.Rd │ │ ├── htmlMutationBatchEffects.Rd │ │ ├── mbatchRunFromConfig.Rd │ │ ├── mutationBatchAssess.Rd │ │ └── mutationBatchExtract.Rd │ ├── tests │ │ ├── buildArchive.R │ │ ├── buildBatchHeatMap_Files.R │ │ ├── buildBatchHeatMap_Structures.R │ │ ├── configError.R │ │ ├── configLength.R │ │ ├── correction_ANOVA_adj.R │ │ ├── correction_ANOVA_unadj.R │ │ ├── correction_EBN_Plus.R │ │ ├── correction_EB_withNonpara.R │ │ ├── correction_EB_withPara.R │ │ ├── correction_MP_batch.R │ │ ├── correction_MP_overall.R │ │ ├── correction_RBN_Pseudoreps.R │ │ ├── correction_RBN_Replicates.R │ │ ├── mbatchRunFromConfig.R │ │ ├── mutationBatchAssess.R │ │ ├── mutationBatchExtract.R │ │ ├── runConfig1.R │ │ ├── runConfig2.R │ │ ├── runConfigHCCHM.R │ │ ├── runConfigMW.R │ │ └── runConfigMW2.R │ └── vignettes │ │ └── MBatchUtils_MakeZipArchive.Rmd └── PyMBatch │ ├── .idea │ ├── .gitignore │ ├── PyMBatch.iml │ ├── copyright │ │ └── PythonCopyright.xml │ ├── inspectionProfiles │ │ ├── Project_Default.xml │ │ └── profiles_settings.xml │ ├── misc.xml │ ├── modules.xml │ ├── other.xml │ ├── pylint.xml │ └── vcs.xml │ ├── README.md │ ├── mbatch.egg-info │ ├── PKG-INFO │ ├── SOURCES.txt │ ├── dependency_links.txt │ ├── requires.txt │ └── top_level.txt │ ├── mbatch │ ├── __init__.py │ ├── batchstats │ │ ├── __init__.py │ │ └── batch_stats.py │ ├── correct │ │ ├── __init__.py │ │ └── correct.py │ ├── dapi │ │ ├── __init__.py │ │ └── query.py │ ├── dsc │ │ ├── __init__.py │ │ ├── dsc_calc.py │ │ ├── dsc_info.py │ │ └── dsc_perm.py │ ├── gdcapi │ │ ├── __init__.py │ │ ├── convert_aliquot.py │ │ ├── convert_case.py │ │ ├── convert_clinical.py │ │ ├── convert_dataset.py │ │ ├── convert_hg38_gene.py │ │ ├── convert_hg38_meth.py │ │ ├── converter_copynumtsv.py │ │ ├── converter_mirnatxt.py │ │ ├── converter_mutationmaf.py │ │ ├── converter_rppatsv.py │ │ ├── converter_scdiff.py │ │ ├── converter_sesamemeth.py │ │ ├── converter_snp6txt.py │ │ ├── converter_starcounts.py │ │ ├── download_biospecimen.py │ │ ├── download_clinical.py │ │ ├── download_datafile.py │ │ ├── download_history_mixin.py │ │ ├── download_sample.py │ │ ├── gdcapi.py │ │ ├── gdcapi_globals.py │ │ └── standardized_data.py │ ├── index │ │ ├── __init__.py │ │ ├── index_api.py │ │ ├── index_entry.py │ │ ├── index_mbatch.py │ │ ├── index_original_data.py │ │ └── index_repos.py │ ├── ldapjwt │ │ ├── __init__.py │ │ └── ldapjwt.py │ ├── legend │ │ ├── __init__.py │ │ └── legend.py │ ├── pipeline │ │ ├── __init__.py │ │ ├── job.py │ │ ├── pipeline.py │ │ └── std_data.py │ ├── stddata │ │ ├── __init__.py │ │ └── stddata.py │ ├── test │ │ ├── __init__.py │ │ ├── common.py │ │ ├── test_dapiquery.py │ │ ├── test_dsc.py │ │ ├── test_index.py │ │ ├── test_job.py │ │ ├── test_ldapjwt.py │ │ ├── test_legend.py │ │ ├── test_pls.py │ │ └── test_volcano.py │ ├── visualindex │ │ ├── __init__.py │ │ ├── visual_index_base.py │ │ ├── visual_index_dsc.py │ │ └── visual_index_kwd.py │ └── volcano │ │ ├── __init__.py │ │ ├── api.py │ │ ├── calc.py │ │ └── plot.py │ ├── scripts │ ├── __init__.py │ ├── analysis_gdc.py │ ├── analysis_gdc_check.py │ ├── analysis_gdc_local.py │ ├── analysis_gdc_reindex.py │ ├── analysis_gdc_update.py │ ├── analysis_mwb.py │ ├── analysis_mwb_check.py │ ├── convert_gdc.py │ ├── convert_gdc_check.py │ ├── correct_gdc_0-check.py │ ├── correct_gdc_1-initiate.py │ ├── correct_gdc_2-continue.py │ ├── index_main.py │ └── legend_main.py │ └── setup.py ├── docker-build ├── BCBbase │ ├── Dockerfile │ ├── README.md │ └── installations │ │ ├── README.txt │ │ ├── ShaidyMapGen.jar │ │ ├── conda.txt │ │ ├── custom.js │ │ ├── installForMBatch0.R │ │ ├── installForMBatch1.R │ │ ├── installForMBatch2.R │ │ ├── installForMBatch3.R │ │ ├── installNGCHM.R │ │ ├── ngchmWidget-min.js │ │ └── postInstall.R └── MBatchImage │ ├── Dockerfile │ ├── Dockerfile_template │ └── docker-compose.yml ├── docker-compose.yml ├── docs ├── MBatch │ ├── MBatch_01_InstallLinux.pdf │ ├── MBatch_01_InstallOSX.pdf │ ├── MBatch_01_InstallWindows.pdf │ ├── MBatch_02_RunningTests.pdf │ ├── MBatch_03_StandardizedData.pdf │ ├── MBatch_03_UserData.pdf │ ├── MBatch_04-00_DSCOutput.pdf │ ├── MBatch_04-00_ParametersBatchTypesValues.pdf │ ├── MBatch_04-01_SupervisedClusteringBatchesStructures.pdf │ ├── MBatch_04-02_PCA_Regular_Structures.pdf │ ├── MBatch_04-03_HierarchicalClustering_Structures.pdf │ ├── MBatch_04-04_Boxplot_Group_Structures.pdf │ ├── MBatch_04-05_CDP_Structures.pdf │ ├── MBatch_04-06_PCA_DualBatch_Structures.pdf │ ├── MBatch_04-07_SupervisedClustering_Pairs_Structures.pdf │ ├── MBatch_04-08_Boxplot_AllSamplesRLE_Structures.pdf │ ├── MBatch_04-09_Boxplot_AllSamplesData_Structures.pdf │ ├── MBatch_04-10_HierarchicalClustering.pdf │ ├── MBatch_04-99_Statistics.pdf │ ├── MBatch_05-01_EBNPlus_CombineBatches.pdf │ ├── MBatch_05-02_EBNPlus_Correction_Structures.pdf │ ├── MBatch_05-03_RBN_Replicates.pdf │ ├── MBatch_05-04_RBN_Pseudoreplicates.pdf │ ├── MBatch_05-05_EB_withNonParametricPriors.pdf │ ├── MBatch_05-06_EB_withParametricPriors.pdf │ ├── MBatch_05-07_MP_Overall.pdf │ ├── MBatch_05-08_MP_ByBatch.pdf │ ├── MBatch_05-09_AN_Adjusted.pdf │ ├── MBatch_05-10_AN_Unadjusted.pdf │ ├── 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