README.md

Analysis Modules

This directory contains various analysis modules in the OpenPedCan project. See the README of an individual analysis modules for more information about that module.

Modules at a glance

The table below is intended to help project organizers quickly get an idea of what files (and therefore types of data) are consumed by each analysis module, what the module does, and what output files it produces that can be consumed by other analysis modules. This is in service of documenting interdependent analyses. Note that nearly all modules use the harmonized clinical data file (histologies.tsv) even when it is not explicitly included in the table below.

Module	Input Files	Brief Description	Produces files for data release?	Output Files Consumed by Other Analyses	OT compatibility	Adapted for OPC?	Run Platform	Action Plan
chromosomal-instability	histologies.tsv sv-manta.tsv.gz cnv-cnvkit.seg.gz	Evaluates chromosomal instability by calculating chromosomal breakpoint densities and by creating circular plot visuals	No	breakpoint-data/union_of_breaks_densities.tsv	No	No	N/A	Will Adapt for OT
chromothripsis	sv-manta.tsv.gz cnv-consensus.seg.gz independent-specimens.wgs.primary-plus.tsv	chromothripsis analysis per #1007	No	N/A	No	No	N/A	N/A
cnv-chrom-plot	cnv-consensus-gistic.zip cnv-consensus.seg	Plots genome wide visualizations relating to copy number results	No	N/A	No	No	N/A	N/A
cnv-comparison	Earlier version of SEG files	Deprecated; compared earlier version of the CNV methods.	No	N/A	No	No	N/A	N/A
cnv-frequencies	histologies.tsv consensus_wgs_plus_cnvkit_wxs.tsv.gz independent-specimens.wgswxspanel.primary.eachcohort.tsv independent-specimens.wgswxspanel.relapse.eachcohort.tsv independent-specimens.wgswxspanel.primary.tsv independent-specimens.wgswxspanel.relapse.tsv	Annotate CNV table with mutation frequencies	No	results/gene-level-cnv-consensus-annotated-mut-freq.jsonl.gz results/gene-level-cnv-consensus-annotated-mut-freq.tsv.gz	Yes	Yes	GitHub	N/A
collapse-rnaseq	gene-expression-rsem-tpm.rds gencode.v27.primary_assembly.annotation.gtf.gz	Collapses RSEM FPKM matrices such that gene symbols are de-duplicated.	Yes	results/gene-expression-rsem-fpkm-collapsed.rds included in data download; too large for tracking via GitHub	Yes	Yes	CAVATICA	N/A
comparative-RNASeq-analysis	gene-expression-rsem-tpm.rds histologies.tsv mend-qc-manifest.tsv mend-qc-results.tar.gz	In progress; will produce expression outlier profiles per #229	No	N/A	No	No	N/A	N/A
compare-gistic	cnv-consensus-gistic.zip analyses/run-gistic/results/cnv-consensus-hgat-gistic.zip analyses/run-gistic/results/cnv-consensus-lgat-gistic.zip analyses/run-gistic/results/cnv-consensus-medulloblastoma-gistic.zip	Comparison of the GISTIC results of the entire cohort with the GISTIC results of three individual histolgies, namely, LGAT, HGAT and medulloblastoma #547	No	N/A	No	No	N/A	N/A
copy_number_consensus_call	cnv-cnvkit.seg.gz cnv-controlfreec.tsv.gz sv-manta.tsv.gz	Produces consensus copy number calls per #128 and a set of excluded regions where CNV calls are not made	Yes	results/cnv_consensus.tsv results/cnv-consensus.seg.gz included in data download ref/cnv_excluded_regions.bed ref/cnv_callable.bed	Yes	Yes	CAVATICA	N/A
create-subset-files	All files	This module contains the code to create the subset files used in continuous integration	No	All subset files for continuous integration	No	No	N/A	Will set up for OT ticket in
efo-mondo-mapping	histologies.tsv efo-mondo-map.tsv	This module contains a file with EFO, MONDO, and NCIT codes for all cancer_group found in histologies.tsv and runs a script to qc in case any cancer_group is missed	Yes	efo-mondo-mapping.tsv	No	Yes	N/A	Yes
filter-mtp-tables	gencode.v38.primary_assembly.annotation.gtf.gz PMTL_v1.1.tsv histologies.tsv gene-level-snv-consensus-annotated-mut-freq.tsv.gz snv-consensus-plus-hotspots.maf.tsv.gz variant-level-snv-consensus-annotated-mut-freq.tsv.gz gene-level-cnv-consensus-annotated-mut-freq.tsv.gz consensus_wgs_plus_cnvkit_wxs.tsv.gz putative-oncogene-fusion-freq.tsv.gz fusion-putative-oncogenic.tsv putative-oncogene-fused-gene-freq.tsv.gz long_n_tpm_mean_sd_quantile_gene_wise_zscore.tsv.gz long_n_tpm_mean_sd_quantile_group_wise_zscore.tsv.gz	Remove Ensembl (ESNG) gene identifier in the OPenPedCan mutation frequency tables, including SNV, CNV, fusion, and TPM expression tables that are not in GENCODE v38 and Ensembl package 104.	No	All files from module results directory	No	Yes	N/A	Yes
focal-cn-file-preparation	cnv-cnvkit.seg.gz cnv-controlfreec.tsv.gz gene-expression-rsem-tpm-collapsed.rds cnv-consensus.seg.gz	Maps from copy number variant caller segments to gene identifiers; will be updated to take into account changes that affect entire cytobands, chromosome arms #186	Yes	results/cnvkit_annotated_cn_wxs_autosomes.tsv.gz results/cnvkit_annotated_cn_wxs_x\_and_y.tsv.gz results/consensus_seg_annotated_cn_autosomes.tsv.gz results/consensus_seg_annotated_cn_x\_and_y.tsv.gz results/consensus_wgs_plus_cnvkit_wxs.tsv.gz included in data download results/consensus_wgs_plus_cnvkit_wxs_autosomes.tsv.gz included in data download results/consensus_wgs_plus_cnvkit_wxs_x\_and_y.tsv.gz included in data download	Yes	Yes	CAVATICA	N/A
fusion_filtering	fusion-arriba.tsv.gz fusion-starfusion.tsv.gz independent-specimens.rnaseq.primary.tsv independent-specimens.rnaseq.relapse.tsv	Standardizes, filters, and prioritizes fusion calls	Yes	results/fusion-putative-oncogenic.tsv included in data download results/fusion-recurrent-fusion-bycancergroup.tsv results/fusion-recurrent-fusion-bysample.tsv results/fusion-recurrently-fused-genes-bycancergroup.tsv results/fusion-recurrently-fused-genes-bysample.tsv	Yes	Yes	GitHub	N/A
fusion-frequencies	histologies.tsv fusion-putative-oncogenic.tsv fusion-dgd.tsv.gz independent-specimens.rnaseqpanel.primary.tsv independent-specimens.rnaseqpanel.relapse.tsv independent-specimens.rnaseqpanel.primary.eachcohort.tsv independent-specimens.rnaseqpanel.relapse.eachcohort.tsv	Gather counts and frequencies for fusion per cancer_group and cohort	results/putative-oncogene-fused-gene-freq.jsonl.gz results/putative-oncogene-fused-gene-freq.tsv.gz results/putative-oncogene-fusion-freq.jsonl.gz results/putative-oncogene-fusion-freq.tsv.gz	N/A	Yes	Yes	GitHub	N/A
fusion-summary	histologies.tsv fusion-putative-oncogenic.tsv fusion-arriba.tsv.gz fusion-starfusion.tsv.gz	Generate summary tables from fusion files (#398; #623)	Yes	results/fusion_summary_embryonal_foi.tsv results/fusion_summary_ependymoma_foi.tsv results/fusion_summary_ewings_foi.tsv	Yes	Yes	GitHub	N/A
gene_match	GTF file sources: gencode v28 gencode v38 open_ped_can_v7_ensg-hugo-rmtl-mapping.tsv	This module reads GTF file and formats attributes to extract gene symbol with gene ensembl ID.	Yes	results\ensg-hugo-pmtl-mapping.tsv	Yes	Yes	GitHub	N/A
gene-set-enrichment-analysis	gene-expression-rsem-tpm-collapsed.rds histologies.tsv	Updated gene set enrichment analysis with appropriate RNA-seq expression data	No	results/gsva_scores.tsv combined file for all RNA library types	Yes	Yes	GitHub	Move to CAVATICA
hotspots-detection	snv-strelka2.vep.maf.gz snv-mutect2.vep.maf.gz snv-vardict.vep.maf.gz snv-lancet.vep.maf.gz	Scavenges cancer any hotspot calls from each caller and merges with consensus (3/3) calls if it was missed in snv-caller workflow.	No	snv-hotspots-mutation.maf.tsv.gz	No	No	CAVATICA	N/A
immune-deconv	gene-expression-rsem-tpm-collapsed.rds	Immune/Stroma characterization across PBTA part of #15	No	results/xcell_output.rds results/quantiseq_output.rds	No	No	N/A	N/A
independent-samples	histologies.tsv	Generates independent specimen lists for WGS/WXS samples	Yes	results/independent-specimens.wgswxspanel.primary.tsv included in data download results/independent-specimens.wgswxspanel.relapse.tsv included in data download results/independent-specimens.wgswxspanel.primary.eachcohort.tsv included in data download results/independent-specimens.wgswxspanel.relapse.eachcohort.tsv included in data download results/independent-specimens.wgswxspanel.primary.prefer.wxs.tsv included in data download results/independent-specimens.wgswxspanel.relapse.prefer.wxs.tsv included in data download results/independent-specimens.wgswxspanel.primary.eachcohort.prefer.wxs.tsv included in data download results/independent-specimens.wgswxspanel.relapse.eachcohort.prefer.wxs.tsv included in data download results/independent-specimens.rnaseq.primary.tsv included in data download results/independent-specimens.rnaseq.relapse.tsv included in data download results/independent-specimens.rnaseq.primary.eachcohort.tsv included in data download results/independent-specimens.rnaseq.relapse.eachcohort.tsv included in data download	Yes	Yes	GitHub	N/A
interaction-plots	independent-specimens.wgs.primary-plus.tsv snv-consensus-mutation.maf.tsv.gz	Creates interaction plots for mutation mutual exclusivity/co-occurrence #13; may be updated to include other data types e.g., fusions	No	N/A	No	No	N/A	N/A
long-format-table-utils	ensg-hugo-rmtl-mapping.tsv analyses/fusion_filtering/references/genelistreference.txt efo-mondo-map.tsv uberon-map-gtex-group.tsv uberon-map-gtex-subgroup.tsv	Functions and scripts for handling long-format tables	No	annotator/annotation-data/ensg-gene-full-name-refseq-protein.tsv annotator/annotation-data/oncokb-cancer-gene-list.tsv	Yes	Yes	GitHub	N/A
methylation-preprocessing	metadata\TARGET_Normal_MethylationArray_20160812.sdrf.txt metadata\TARGET_NBL_MethylationArray_20160812.sdrf.1.txt TARGET_NBL_MethylationArray_20160812.sdrf.2.txt metadata/TARGET_CCSK_MethylationArray_20160819.sdrf.txt metadata\TARGET_OS_MethylationArray_20161103.sdrf.txt metadata\TARGET_WT_MethylationArray_20160831.sdrf.txt metadata\TARGET_AML_MethylationArray_20160812_450k.sdrf.1.txt metadata\TARGET_AML_MethylationArray_20160812_450k.sdrf.2.txt metadata\TARGET_AML_MethylationArray_20160812_27k.sdrf.1.txt metadata\TARGET_AML_MethylationArray_20160812_27k.sdrf.2.txt metadata\TARGET_AML_MethylationArray_20160812_27k.sdrf.3.txt metadata\manifest_methylation_CBTN_20220410.1.csv metadata\manifest_methylation_CBTN_20220410.2.csv metadata\manifest_methylation_CBTN_20220410.3.csv metadata\manifest_methylation_CBTN_20220410.4.csv	Preprocess probe hybridization intensity values of selected methylated and unmethylated cytosine (CpG) loci into usable methylation measurements for the Pediatric Open Targets, OPenPedCan-analysis raw DNA methylation array datasets.	No	N/A	Yes	Yes	GitHub	N/A
molecular-subtyping-ATRT	analyses/gene-set-enrichment-analysis/results/gsva_scores.tsv gene-expression-rsem-tpm-collapsed.rds analyses/focal-cn-file-preparation/results/consensus_seg_annotated_cn_autosomes.tsv.gz snv-consensus-mutation-tmb-all.tsv cnv-consensus-gistic.zip	Deprecated; Summarizing data into tabular format in order to molecularly subtype ATRT samples #244; this analysis did not work	No	N/A	No	No	N/A	N/A
molecular-subtyping-CRANIO	histologies-base.tsv snv-consensus-plus-hotspots.maf.tsv.gz	Molecular subtyping of craniopharyngiomas samples #810	No	results/CRANIO_molecular_subtype.tsv	No	No	N/A	Prepare for scaling
molecular-subtyping-EPN	histologies-base.tsv gene-expression-rsem-tpm-collapsed.rds analyses/chromosomal-instability/breakpoint-data/union_of_breaks_densities.tsv analyses/fusion-summary/results/fusion_summary_ependymoma_foi.tsv analyses/gene-set-enrichment-analysis/results/gsva_scores.tsv	molecular subtyping of ependymoma tumors	No	results/EPN_all_data_withsubgroup.tsv	No	No	N/A	Will Adapt for OT
molecular-subtyping-EWS	histologies-base.tsv analyses/fusion-summary/results/fusion_summary_ewings_foi.tsv	Reclassification of tumors based on the presence of defining fusions for Ewing Sarcoma per #623	No	results/EWS_samples.tsv	No	No	N/A	Will Adapt for OT
molecular-subtyping-HGG	histologies-base.tsv snv-consensus-plus-hotspots.maf.tsv.gz consensus_wgs_plus_cnvkit_wxs.tsv.gz fusion-putative-oncogenic.tsv cnv-consensus-gistic.zip gene-expression-rsem-tpm-collapsed.rds tp53_altered_status.tsv	Molecular subtyping of high-grade glioma samples #249	No	results/HGG_molecular_subtype.tsv	Yes	Yes	GitHub	N/A
molecular-subtyping-LGAT	histologies-base.tsv snv-consensus-plus-hotspots.maf.tsv.gz fusion-putative-oncogenic.tsv analyses/fusion_filtering/results/fusion-recurrently-fused-genes-bysample.tsv	Molecular subtyping of Low-grade astrocytic tumor samples #631	No	results/lgat_subtyping.tsv	Yes	Yes	GitHub	N/A
molecular-subtyping-MB	histologies.tsv gene-expression-rsem-tpm-collapsed.rds	Molecular classification of Medulloblastoma subtypes part of #116	No	results/MB_molecular_subtype.tsv	Yes	Yes	GitHub	N/A
molecular-subtyping-SHH-tp53	histologies snv-consensus-plus-hotspots.maf.tsv.gz	Deprecated; Identify the SHH-classified medulloblastoma samples that have TP53 mutations #247	No	N/A	No	No	N/A	N/A
molecular-subtyping-chordoma	analyses/focal-cn-file-preparation/results/consensus_seg_annotated_cn_autosomes.tsv.gz gene-expression-rsem-fpkm-collapsed.stranded.rds	identifying poorly-differentiated chordoma samples per #250	No	N/A	No	No	N/A	Will Adapt for OT
molecular-subtyping-embryonal	histologies-base.tsv analyses/fusion-summary/fusion_summary_embryonal_foi.tsv sv-manta.tsv.gz consensus_wgs_plus_cnvkit_wxs.tsv.gz analyses/focal-cn-file-preparation/cnvkit_annotated_cn_x\_and_y.tsv.gz analyses/focal-cn-file-preparation/controlfreec_annotated_cn_x\_and_y.tsv.gz gene-expression-rsem-tpm-collapsed.rds	Molecular subtyping of non-medulloblastoma, non-ATRT embryonal tumors #251	No	results/embryonal_tumor_molecular_subtypes.tsv	No	No	N/A	Will Adapt for OT
molecular-subtyping-integrate	histologies-base.tsv results/compiled_molecular_subtypes_with_clinical_pathology_feedback.tsv	Add molecular subtype information to base histology	No	results/histologies.tsv	Yes	Yes	GitHub	N/A
molecular-subtyping-neurocytoma	histologies-base.tsv	Molecular subtyping of Neurocytoma samples #805	No	results/neurocytoma_subtyping.tsv	No	No	N/A	Will Adapt for OT
molecular-subtyping-pathology	analyses/molecular-subtyping-CRANIO/results/CRANIO_molecular_subtype.tsv analyses/molecular-subtyping-EPN/results/CRANIO_molecular_subtype.tsv analyses/molecular-subtyping-MB/results/MB_molecular_subtype.tsv analyses/molecular-subtyping-neurocytoma/results/neurocytoma_subtyping.tsv analyses/molecular-subtyping-EWS/results/EWS_samples.tsv analyses/molecular-subtyping-HGG/results/HGG_molecular_subtype.tsv analyses/molecular-subtyping-LGAT/results/lgat_subtyping.tsv analyses/molecular-subtyping-embryonal/results/embryonal_tumor_molecular_subtypes.tsv	Compile output from other molecular subtyping modules and incorporate pathology feedback #645	No	results/compiled_molecular_subtyping_with_clinical_feedback.tsv results/compiled_molecular_subtypes_with_clinical_pathology_feedback.tsv	Yes	Yes	GitHub	N/A
mutational-signatures	snv-consensus-plus-hotspots.maf.tsv.gz	Performs COSMIC and Alexandrov et al. mutational signature analysis using the consensus SNV data	No	N/A	No	No	N/A	N/A
mutect2-vs-strelka2	snv-mutect2.vep.maf.gz snv-strelka2.vep.maf.gz	Deprecated; comparison of only two SNV callers, subsumed by snv-callers	No	N/A	No	No	N/A	N/A
oncoprint-landscape	snv-consensus-plus-hotspots.maf.tsv.gz fusion-putative-oncogenic.tsv analyses/focal-cn-file-preparation/results/controlfreec_annotated_cn_autosomes.tsv.gz independent-specimens.\*	Combines mutation, copy number, and fusion data into an OncoPrint plot #6; will need to be updated as all data types are refined	No	N/A	No	No	N/A	N/A
pedcbio-cnv-prepare	consensus_wgs_plus_cnvkit_wxs_autosomes.tsv.gz consensus_wgs_plus_cnvkit_wxs_x\_and_y.tsv.gz	Generate annotated CNV files that are similar to seg files for PedCBio uploads to include all samples with neutral CNV calls	Yes	Upload to PedCBio S3 bucket for ingestion	Yes	GitHub	N/A
pedcbio-sample-name	histologies.tsv input\cbtn_cbio_sample.csv input\dgd_cbio_sample.csv input\oligo_nation_cbio_sample.csv input\x01_fy16_nbl_maris_cbio_sample.csv	For some of the samples, when multiple DNA or RNA specimens are associated with the same sample, there is no column that would distinguish between different aliquots while still tying DNA and RNA together.	Yes	Upload to PedCBio S3 bucket for ingestion	Yes	GitHub	N/A
pedot-table-column-display-order-name	analyses/snv-frequencies/results/gene-level-snv-consensus-annotated-mut-freq.tsv analyses/snv-frequencies/results/variant-level-snv-consensus-annotated-mut-freq.tsv.gz analyses/cnv-frequencies/results/gene-level-cnv-consensus-annotated-mut-freq.tsv.gz analyses/fusion-frequencies/results/putative-oncogene-fused-gene-freq.tsv.gz analyses/fusion-frequencies/results/putative-oncogene-fusion-freq.tsv.gz analyses/rna-seq-expression-summary-stats/results/long_n\_tpm_mean_sd_quantile_gene_wise_zscore.tsv.gz analyses/rna-seq-expression-summary-stats/results/long_n\_tpm_mean_sd_quantile_group_wise_zscore.tsv.gz	Generate and validate an Excel spreadsheet for Pediatric Open Targets PedOT website table display orders and names	No	Upload to FNL BOX	Yes	Yes	GitHub	N/A
rna-seq-composition	gene-expression-rsem-tpm.rds histologies.tsv mend-qc-results.tar.gz mend-qc-manifest.tsv star-log-manifest.tsv star-log-final.tar.gz	Analyzes the fraction of read types that comprise each RNA-Seq sample; flags samples with unusual composition	No	N/A	No	No	N/A	N/A
rna-seq-protocol-ruvseq	gene-counts-rsem-expected_count-collapsed.rds	Evaluate the use of empirical negative control genes for batch correction	No	N/A	Yes	Yes	Github	N/A
rna-seq-protocol-dge	gene-counts-rsem-expected_count-collapsed.rds	In progress #17; check if the DGE analysis between poly-A and stranded RNA-seq data follow a null-p-value distribution; determine stably expressed genes between poly-A and stranded samples.	No	N/A	Yes	Yes	GitHub	N/A
rna-seq-expression-summary-stats	gene-expression-rsem-tpm-collapsed.rds histologies.tsv	Calculate TPM summary statistics within each cancer group and cohort. #51.	No	Upload to FNL Box	Yes	Yes	GitHub	N/A
run-gistic	histologies.tsv cnv-consensus.seg.gz	Runs GISTIC 2.0 on SEG files	Yes	cnv-consensus-gistic.zip included in data download	Yes	Yes	GitHub	Move to CAVATICA
sample-distribution-analysis	histologies.tsv	Produces plots and tables that illustrate the distribution of different histologies in the PBTA data	No	N/A	No	No	N/A	N/A
selection-strategy-comparison	gene-expression-rsem-tpm-collapsed.rds	Deprecated; Comparison of RNA-seq data from different selection strategies	No	N/A	No	No	N/A	N/A
sex-prediction-from-RNASeq	gene-expression-kallisto.stranded.rds histologies.tsv	predicts genetic sex using RNA-seq data #84	No	N/A	No	No	N/A	N/A
snv-callers	snv-lancet.vep.maf.gz snv-mutect2.vep.maf.gz snv-strelka2.vep.maf.gz snv-vardict.vep.maf.gz tcga-snv-lancet.vep.maf.gz tcga-snv-mutect2.vep.maf.gz tcga-snv-strelka2.vep.maf.gz	Generates consensus SNV and indel calls for PBTA and TCGA data; calculates tumor mutation burden using the consensus calls	Yes	results/consensus/snv-consensus-plus-hotspots.maf.tsv included in data download; too large for tracking via GitHub results/consensus/snv-consensus-mutation-tmb-all.tsv results/consensus/snv-consensus-mutation-tmb-coding.tsvincluded in data download; too large for tracking via GitHub results/consensus/tcga-snv-consensus-mutation.maf.tsv.gz results/consensus/tcga-snv-mutation-tmb.tsv results/consensus/tcga-snv-mutation-tmb-coding.tsv	No	N/A	N/A
snv-frequencies	histologies.tsv snv-consensus-plus-hotspots.maf.tsv.gz snv-dgd.maf.tsv.gz independent-specimens.wgswxspanel.primary.eachcohort.prefer.wxs.tsv independent-specimens.wgswxspanel.relapse.eachcohort.prefer.wxs.tsv independent-specimens.wgswxspanel.primary.prefer.wxs.tsv independent-specimens.wgswxspanel.relapse.prefer.wxs.tsv	Annotate SNV table with mutation frequencies	No	results/gene-level-snv-consensus-annotated-mut-freq.jsonl.gz results/gene-level-snv-consensus-annotated-mut-freq.tsv.gz variant-level-snv-consensus-annotated-mut-freq.jsonl.gz variant-level-snv-consensus-annotated-mut-freq.tsv.gz	Yes	Yes	GitHub	N/A
ssgsea-hallmark	gene-counts-rsem-expected_count-collapsed.rds	Deprecated; performs GSVA using Hallmark gene sets	No	N/A	No	No	N/A	N/A
survival-analysis	TBD	In progress; will eventually contain functions for various types of survival analysis #18	No	N/A	No	No	N/A	N/A
telomerase-activity-prediction	gene-expression-rsem-tpm-collapsed.rds gene-counts-rsem-expected_count-collapsed.rds	Quantify telomerase activity across pediatric brain tumors part of #148	No	results/TelomeraseScores_PTBAPolya_counts results/TelomeraseScores_PTBAPolya_FPKM.txt results/TelomeraseScores_PTBAStranded_counts.txt results/TelomeraseScores_PTBAStranded_FPKM.txt	No	No	N/A	N/A
tmb-calculation	gencode.v27.primary_assembly.annotation.bed intersect_strelka_mutect2_vardict_WGS.bed snv-consensus-plus-hotspots.maf.tsv.gz biospecimen_id_to_bed_map.tsv histologies-base.tsv hg38_strelka.bed wgs_canonical_calling_regions.hg38.bed gencode.v27.primary_assembly.annotation.gtf.gz	The Tumor Mutation Burden calculation is adapted from snv-callers module of the OpenPBTA-analyses, and use the SNV calls Mutect2, Strelka2, Lancet, and Vardict callers.	No	N/A	No	No	N/A	N/A
tmb-compare	snv-consensus-mutation-tmb-coding.tsv	Compares PBTA tumor mutation burden to adult TCGA data. The D3B TMB calculations TMB_d3b_code and its comparison notebook compare-tmb-calculations.Rmd are deprecated.	No	N/A	No	No	N/A	N/A
tp53_nf1_score	snv-consensus-plus-hotspots.maf.tsv gene-expression-rsem-tpm-collapsed.rds consensus_wgs_plus_cnvkit_wxs.tsv.gz	Applies TP53 inactivation, NF1 inactivation, and Ras activation classifiers to RNA-seq data #165	No	TP53_NF1_snv_alteration.tsv gene-expression-rsem-tpm-collapsed_classifier_scores.tsv loss_overlap_domains_tp53.tsv poly-A_TP53.png stranded_TP53.png sv_overlap_tp53.tsv tp53_altered_status.tsv	Yes	Yes	GitHub	N/A
transcriptomic-dimension-reduction	gene-expression-rsem-tpm.rds gene-expression-kallisto.rds	Dimension reduction and visualization of RNA-seq data part of #9	No	N/A	No	No	N/A	N/A
tcga-capture-kit-investigation	snv-lancet.vep.maf.gz snv-mutect2.vep.maf.gz snv-strelka2.vep.maf.gz tcga-snv-lancet.vep.maf.gz tcga-snv-mutect2.vep.maf.gz tcga-snv-strelka2.vep.maf.gz histologies.tsv tcga-manifest.tsv WGS.hg38.lancet.unpadded.bed WGS.hg38.strelka2.unpadded.bed WGS.hg38.mutect2.vardict.unpadded.bed	Investigation of the TMB discrepancy between PBTA and TCGA data	No	results/*.bed	Yes	No	GitHub	N/A
tumor-gtex-plots	gene-expression-rsem-tpm-collapsed.rds histologies.tsv	In progress #38; tumor vs normal and tumor only expression plots	No	results/pan_cancer_plots_cancer_group_level.{tsv, jsonl.gz} results/pan_cancer_plots_cohort_cancer_group_level.{tsv, jsonl.gz} results/tumor_normal_gtex_plots_cancer_group_level.{tsv, jsonl.gz} results/tumor_normal_gtex_plots_cohort_cancer_group_level.{tsv, jsonl.gz} results/metadata.tsv plots/\*.png	Yes	Yes	GitHub	N/A
tumor-normal-differential-expression	histologies.tsv gene-counts-rsem-expected_count-collapsed.rds independent-specimens.rnaseq.primary.tsv independent-specimens.rnaseq.primary.eachcohort.tsv gene-expression-rsem-tpm-collapsed.rds ensg-hugo-pmtl-mapping.tsv efo-mondo-map.tsv uberon-map-gtex-subgroup.tsv	This module takes as input histologies and the RNA-Seq expression matrices data, and performs differential expression analysis for all combinations of GTEx subgroup normal and cancer histology type tumor.	No	N/A	Yes	Yes	HPC CAVATICA user can create application for personal analysis purpose using scripts provided in the module	N/A