analyses

Analysis Modules

This directory contains various analysis modules in the OpenPBTA 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	Output Files Consumed by Other Analyses	Modules Consume Outputs	OT compatibility	In Use	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	breakpoint-data/union_of_breaks_densities.tsv	molecular-subtyping-EPN	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	N/A	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	N/A	N/A	No	No	N/A	N/A
cnv-comparison	Earlier version of SEG files	Deprecated; compared earlier version of the CNV methods.	N/A	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	results/gene-level-cnv-consensus-annotated-mut-freq.jsonl.gz results/gene-level-cnv-consensus-annotated-mut-freq.tsv.gz	Upload to FNL BOX	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.	results/gene-expression-rsem-fpkm-collapsed.rds (included in data download; too large for tracking via GitHub)	N/A	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	N/A	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	N/A	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	results/cnv_consensus.tsv results/cnv-consensus.seg.gz (included in data download) ref/cnv_excluded_regions.bed ref/cnv_callable.bed	focal-cn-file-preparation run-gistic	Yes	Yes	CAVATICA	N/A
create-subset-files	All files	This module contains the code to create the subset files used in continuous integration	All subset files for continuous integration	All	No	No	N/A	Will set up for OT (ticket in)
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)	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)	molecular-subtyping-ATRT molecular-subtyping-chordoma molecular-subtyping-embryonal molecular-subtyping-HGG cnv-frequencies	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	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	fusion-summary fusion-frequencies molecular-subtyping-HGG molecular-subtyping-LGAT oncoprint-landscape pedot-table-column-display-order-name	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)	results/fusion_summary_embryonal_foi.tsv results/fusion_summary_ependymoma_foi.tsv results/fusion_summary_ewings_foi.tsv	molecular-subtyping-EPN molecular-subtyping-EWS molecular-subtyping-embryonal	Yes	Yes	GitHub	N/A
fusion-frequencies	fusion-putative-oncogenic.tsv independent-specimens.rnaseq.primary.eachcohort.tsv independent-specimens.rnaseq.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	Upload to FNL BOX	Yes	Yes	GitHub	N/A
gene-set-enrichment-analysis	gene-expression-rsem-tpm-collapsed.rds	Updated gene set enrichment analysis with appropriate RNA-seq expression data	results/gsva_scores.tsv combined file for all RNA library types	molecular-subtyping-ATRT molecular-subtyping-EPN	Yes	Yes	GitHub	Move to CAVATICA
hotspot-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.	snv-hotspots-mutation.maf.tsv.gz	snv-caller	No	No	CAVATICA	N/A
immune-deconv	gene-expression-rsem-tpm-collapsed.rds	Immune/Stroma characterization across PBTA (part of #15)	results/deconv-output.RData	N/A	No	No	N/A	N/A
independent-samples	histologies.tsv	Generates independent specimen lists for WGS/WXS samples	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)	interaction-plots oncoprint-landscape chromothripsis cnv-frequencies fusion-filtering fusion-frequencies snv-frequencies rna-seq-expression-summary-stats	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)	N/A	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	annotator/annotation-data/ensg-gene-full-name-refseq-protein.tsv annotator/annotation-data/oncokb-cancer-gene-list.tsv	snv-frequencies cnv-frequencies fusion-frequencies rna-seq-expression-summary-stats	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	N/A	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	results/CRANIO_molecular_subtype.tsv	molecular-subtyping-pathology	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	results/EPN_all_data_withsubgroup.tsv	molecular-subtyping-pathology	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	results/EWS_samples.tsv	molecular-subtyping-pathology	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	results/HGG_molecular_subtype.tsv	molecular-subtyping-pathology	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	results/lgat_subtyping.tsv	molecular-subtyping-pathology	Yes	Yes	GitHub	N/A
molecular-subtyping-MB	histologies.tsv gene-expression-rsem-tpm-collapsed.rds	Molecular classification of Medulloblastoma subtypes (part of #116)	results/MB_molecular_subtype.tsv	molecular-subtyping-pathology	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	N/A	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	N/A	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	results/embryonal_tumor_molecular_subtypes.tsv	molecular-subtyping-pathology	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	results/histologies.tsv	data release	Yes	Yes	GitHub	N/A
molecular-subtyping-neurocytoma	histologies-base.tsv	Molecular subtyping of Neurocytoma samples #805	results/neurocytoma_subtyping.tsv	molecular-subtyping-pathology	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	results/compiled_molecular_subtyping_with_clinical_feedback.tsv results/compiled_molecular_subtypes_with_clinical_pathology_feedback.tsv	molecular-subtyping-integrate	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	N/A	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	N/A	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	N/A	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	Upload to PedCBio S3 bucket for ingestion	Yes	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	N/A	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	N/A	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	N/A
rna-seq-protocol-dge	gene-counts-rsem-expected_count-collapsed.rds	In progress PediatricOpenTargets/ticket-tracker#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.	N/A	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. PediatricOpenTargets/ticket-tracker#51.	N/A	Upload to FNL Box	Yes	Yes	GitHub	N/A
run-gistic	histologies.tsv cnv-consensus.seg.gz	Runs GISTIC 2.0 on SEG files	cnv-consensus-gistic.zip (included in data download)	cnv-chrom-plot compare-gistic molecular-subtyping-ATRT molecular-subtyping-HGG	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	N/A	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	N/A	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)	N/A	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	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.tsv(included 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	No	N/A	N/A
snv-frequencies	histologies.tsv snv-consensus-plus-hotspots.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	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	Upload to FNL BOX	Yes	Yes	GitHub	N/A
oncoprint-landscape	histologies.tsv snv-consensus-plus-hotspots.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	oncoprint-landscape tp53_nf1_score molecular-subtyping-CRANIO molecular-subtyping-HGG molecular-subtyping-LGAT molecular-subtyping-SHH-tp53 mutational-signatures	N/A	Yes	Yes	GitHub	N/A
ssgsea-hallmark	gene-counts-rsem-expected_count-collapsed.rds	Deprecated; performs GSVA using Hallmark gene sets	N/A	N/A	No	No	N/A	N/A
survival-analysis	TBD	In progress; will eventually contain functions for various types of survival analysis (#18)	N/A	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)	results/TelomeraseScores_PTBAPolya_counts results/TelomeraseScores_PTBAPolya_FPKM.txt results/TelomeraseScores_PTBAStranded_counts.txt results/TelomeraseScores_PTBAStranded_FPKM.txt	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.	N/A	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	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	molecular-subtyping-HGG	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)	N/A	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	results/*.bed	N/A	Yes	No	GitHub	N/A
tumor-gtex-plots	gene-expression-rsem-tpm-collapsed.rds histologies.tsv	In progress PediatricOpenTargets/ticket-tracker#38; tumor vs normal and tumor only expression plots	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	N/A	Yes	Yes	GitHub	N/A