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	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	N/A	Will Adapt for OT
chromothripsis	sv-manta.tsv.gz cnv-consensus.seg.gz independent-specimens.wgs.primary-plus.tsv	Performs chromothripsis analysis	No	N/A	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	N/A	N/A
cnv-frequencies (MTP-specific)	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	Annotates CNV table with frequencies	No	results/gene-level-cnv-consensus-annotated-mut-freq.jsonl.gz results/gene-level-cnv-consensus-annotated-mut-freq.tsv.gz	Yes	GitHub	N/A
collapse-rnaseq (ported to CAVATICA)	gene-expression-rsem-tpm.rds gencode.v39.primary_assembly.annotation.gtf.gz	Collapses RSEM count and TPM 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	CAVATICA	N/A
copy_number_consensus_call	cnv-cnvkit.seg.gz cnv-controlfreec.tsv.gz sv-manta.tsv.gz	Produces consensus copy number calls and a set of excluded regions where CNV calls are not made	Yes	results/cnv_consensus.tsv 'results/uncalled_samples.tsv' results/cnv-consensus.seg.gz included in data download ref/cnv_excluded_regions.bed ref/cnv_callable.bed	Yes	CAVATICA	N/A
create-subset-files	All files	This module contains the code to create the subset files used in GitHub Actions	No	All subset files for continuous integration	No	N/A	Will set up for OT ticket in
data-pre-release-qc	histologies-base.tsv gene-counts-rsem-expected_count-collapsed.rds gene-expression-rsem-tpm-collapased.rds tcga-gene-counts-rsem-expected_count-collapsed.rds tcga-gene-expression-rsem-tpm-collapsed.rds cnv-cnvkit.seg.gz cnvkit_with_status.tsv consensus_wgs_plus_cnvkit_wxs_autosomes.tsv.gz consensus_wgs_plus_cnvkit_wxs_x_and_y.tsv.gz snv-mutation-tmb-all.tsv fusion_summary_embryonal_foi.tsv fusion_summary_ependymoma_foi.tsv fusion_summary_lgg_hgg_foi.tsv fusion_summary_ewings_foi.tsv biospecimen_id_to_bed_map.txt	Performs QC on data pre-release files with requirements which should pass before hand off between BIXU Engineering team to the OpenPedCan team	Yes	'data-pre-release-qc.nb.html'	No	N/A	N/A
efo-mondo-mapping (MTP-specific)	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	Yes	N/A	Yes
filter-mtp-tables (MTP-specific)	gencode.v39.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	Removes Ensembl (ESNG) gene identifier in the OpenPedCan mutation frequency tables, including SNV, CNV, fusion, and TPM expression tables that are not in GENCODE v39 and Ensembl package 104.	No	All files from module results directory	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	Yes	cnvkit_annotated_cn_wxs_autosomes.tsv.gz cnvkit_annotated_cn_wxs_x_and_y.tsv.gz consensus_seg_annotated_cn_autosomes.tsv.gz consensus_seg_annotated_cn_x_and_y.tsv.gz consensus_seg_most_focal_fn_status.tsv.gz consensus_seg_recurrent_focal_cn_units.tsv consensus_seg_with_ucsc_cytoband_status.tsv.gz consensus_wgs_plus_cnvkit_wxs_autosomes.tsv.gzincluded in data download consensus_wgs_plus_cnvkit_wxs_x_and_y.tsv.gz` included in data download	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	GitHub	N/A
fusion-frequencies (MTP-specific)	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	Gathers counts and frequencies for fusion per cancer_group and cohort	No	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	Yes	GitHub	N/A
fusion-summary	histologies.tsv fusion-putative-oncogenic.tsv fusion-arriba.tsv.gz fusion-starfusion.tsv.gz	Generates summary matrices of fusions in preparation for molecular subtyping	Yes	results/fusion_summary_embryonal_foi.tsv results/fusion_summary_ependymoma_foi.tsv results/fusion_summary_ewings_foi.tsv	Yes	GitHub	N/A
gene_match (MTP-specific)	GTF file sources: gencode v28 gencode v38 open_ped_can_v7_ensg-hugo-rmtl-mapping.tsv	Reads GTF file and formats attributes to extract gene symbol with gene ensembl ID.	Yes	ensg-hugo-pmtl-mapping.tsv	Yes	GitHub	N/A
gene-set-enrichment-analysis	gene-expression-rsem-tpm-collapsed.rds histologies.tsv	Performs gene set enrichment analysis by RNA library	No	results/gsva_scores.tsv combined file for all RNA library types	Yes	GitHub	Move to CAVATICA
immune-deconv	gene-expression-rsem-tpm-collapsed.rds data/histologies.tsv	Performs immune cell deconvolution using Xcell and quantiseq	No	xcell_output.rds quantiseq_output.rds	No	N/A	N/A
independent-samples	histologies.tsv	Generates independent specimen lists by experimental strategy and/or cohort	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	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	No	N/A	No	N/A	N/A
long-format-table-utils (MTP-specific)	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	GitHub	N/A
methylation-preprocessing (ported to CAVATICA)	TARGET_Normal_MethylationArray_20160812.sdrf.txt TARGET_NBL_MethylationArray_20160812.sdrf.1.txt TARGET_NBL_MethylationArray_20160812.sdrf.2.txt TARGET_CCSK_MethylationArray_20160819.sdrf.txt TARGET_OS_MethylationArray_20161103.sdrf.txt TARGET_WT_MethylationArray_20160831.sdrf.txt TARGET_AML_MethylationArray_20160812_450k.sdrf.1.txt TARGET_AML_MethylationArray_20160812_450k.sdrf.2.txt TARGET_AML_MethylationArray_20160812_27k.sdrf.1.txt TARGET_AML_MethylationArray_20160812_27k.sdrf.2.txt TARGET_AML_MethylationArray_20160812_27k.sdrf.3.txt manifest_methylation_CBTN_20220410.1.csv manifest_methylation_CBTN_20220410.2.csv manifest_methylation_CBTN_20220410.3.csv manifest_methylation_CBTN_20220410.4.csv	Preprocesses probe hybridization intensity values of selected methylated and unmethylated cytosine (CpG) loci into usable methylation measurements (m-values, beta values, and cnvs).	No	N/A	Yes	Cavatica	N/A
methylation-summary (ported to CAVATICA)	infinium.gencode.v39.probe.annotations.tsv.gz independent-specimens.rnaseqpanel.eachchort.tsv independent-specimens.methyl.eachcohort.tsv gene-expression-rsem-tpm-collapsed.rds rna-isoform-expression-rsem-tpm.rds methyl-beta-values.rds efo-mondo-map.tsv histlogies.tsv	Summarizes preprocessed Illumina Infinium Human Methylation array measurements produced by methylation preprocessing using Illumina infinium methylation array CpG probe coordinates.	No	N/A	No	aws	N/A
molecular-subtyping-ATRT	histologies-base.tsv	Molecular subtyping of ATRTs	No	NA	GitHub	N/A
molecular-subtyping-CRANIO	histologies-base.tsv snv-consensus-plus-hotspots.maf.tsv.gz	Molecular subtyping of craniopharyngiomas	No	results/CRANIO_molecular_subtype.tsv	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 ependymomas	No	results/EPN_all_data_withsubgroup.tsv	No	N/A	Will Adapt for OT
molecular-subtyping-EWS	histologies-base.tsv analyses/fusion-summary/results/fusion_summary_ewings_foi.tsv	Reclassifies tumors based on the presence of defining fusions for Ewing Sarcomas	No	results/EWS_samples.tsv	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 gliomas	No	results/HGG_molecular_subtype.tsv	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 gliomas	No	results/lgat_subtyping.tsv	Yes	GitHub	N/A
molecular-subtyping-MB	histologies-base.tsv gene-expression-rsem-tpm-collapsed.rds	Molecular classification of medulloblastomas	No	results/MB_molecular_subtype.tsv	Yes	GitHub	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	identifies poorly-differentiated chordomas	No	N/A	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	No	results/embryonal_tumor_molecular_subtypes.tsv	No	N/A	Will Adapt for OT
molecular-subtyping-integrate	histologies-base.tsv results/compiled_molecular_subtypes_with_clinical_pathology_feedback.tsv	Adds molecular subtype information to the base histology file	No	results/histologies.tsv	Yes	GitHub	N/A
molecular-subtyping-NBL	histologies-base.tsv consensus_wgs_plus_cnvkit_wxs.tsv.gz cnv-cnvkit.seg.gz cnv-controlfreec.tsv.gz gene-expression-rsem-tpm-collapsed.rds analyses/molecular-subtyping-NBL/input/gmkf_patient_clinical_mycn_status.tsv analyses/molecular-subtyping-NBL/input/target_patient_clinical_mycn_status.tsv	Molecular subtyping of neuroblastomas	No	results/NBL_MYCN_Subtype.tsv results/Alteration_Table.tsv results/Subtypes_Based_On_Cutoff.tsv results/QC_table.tsv	Yes	EC2	N/A
molecular-subtyping-neurocytoma	histologies-base.tsv	Molecular subtyping of neurocytomas	No	results/neurocytoma_subtyping.tsv	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	Compiles output from other molecular subtyping modules and incorporate pathology feedback	No	choroid_plexus_papilloma_subtypes.tsv cns-lymphoma-subtypes.tsv compiled_molecular_subtypes.tsv compiled_molecular_subtypes_and_report_info.tsv compiled_molecular_subtypes_with_clinical_feedback_and_report_info.tsv compiled_molecular_subtypes_with_clinical_pathology_feedback_and_report_info.tsv cranio_adam_subtypes.tsv glialneuronal_tumor_subtypes.tsv juvenile-xanthogranuloma-subtypes.tsv lgat-pathology-free-text-subtypes.tsv meningioma_subtypes.tsv	Yes	GitHub	N/A
molecular-subtyping-PB	histologies-base.tsv	Molecular subtyping of pineoblastomas	No	results/pineo-molecular-subtypes.tsv	Yes	GitHub	N/A
mtp-annotations (MTP-specific)	scratch/mtp-json/targets/ scratch/mtp-json/diseases/	Transforms the OpenTargets Platform Target (core annotations for targets) and Disease/Phenotype (core annotations for diseases and phenotypes) tables into mapping files utilized in filtering MTP designated tables and OPC data release files for plotting API development	No	N/A	local	N/A	N/A
mtp-tables-qc-checks (MTP-specific)	gene-level-cnv-consensus-annotated-mut-freq.tsv.gz gene-level-snv-consensus-annotated-mut-freq.tsv.gz gene-variant-snv-consensus-annotated-mut-freq.tsv.gz putative-oncogene-gused-gene-freq.tsv.gz putative-oncogene-fusion-freq.tsv.gz long_n_tpm_mean_sd_quantitle_gene_wise_zscore.tsv.gz long_n_tpm_mean_sd_quatile_group_wise_zscore.tsv.gz	Performs summary and QC checks comparing the current and the previous OPC mutation frequencies table	No	N/A	No	N/A	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	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	No	N/A	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	Generates 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	GitHub	N/A	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	Formats sample names for pedcbio when multiple DNA or RNA specimens are associated with the same sample	Yes	Upload to PedCBio S3 bucket for ingestion	GitHub	N/A	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	Generates and validates an Excel spreadsheet for Pediatric Open Targets PedOT website table display orders and names	No	Upload to FNL BOX	Yes	GitHub	N/A
rnaseq-batch-correct	gene-counts-rsem-expected_count-collapsed.rds histologies.tsv hk_genes_normals.rds [positive_control_genes].rds	Performs RUVseq-DESeq2 batch-corrected DGE analysis	Yes	N/A	Yes	Github	N/A
rna-seq-expression-summary-stats (MTP-specific)	gene-expression-rsem-tpm-collapsed.rds histologies.tsv	Calculates TPM summary statistics within each cancer group and cohort. #51.	No	Upload to FNL Box	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	GitHub	Move to CAVATICA
snv-frequencies (MTP-specific)	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	Annotates 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	GitHub	N/A
survival-analysis	TBD	Contains survival analysis templates	No	N/A	No	N/A	N/A
telomerase-activity-prediction	gene-expression-rsem-tpm-collapsed.rds gene-counts-rsem-expected_count-collapsed.rds	Quantifies telomerase activity using RNA-Seq	No	results/TelomeraseScores_PTBAPolya_counts results/TelomeraseScores_PTBAPolya_FPKM.txt results/TelomeraseScores_PTBAStranded_counts.txt results/TelomeraseScores_PTBAStranded_FPKM.txt	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.v39.primary_assembly.annotation.gtf.gz	Calculates TMB using consensus SNV calls for tumors with paired T/N variant calls only	Yes	snv-mutation-tmb-all.tsv snv-mutation-tmb-coding.tsv	Yes	GitHub	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 classifier to RNA-Seq data	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	GitHub	N/A
transcriptomic-dimension-reduction	gene-expression-rsem-tpm.rds gene-expression-kallisto.rds	Performs dimension reduction and visualization of RNA-seq data	No	N/A	No	N/A	N/A
tumor-gtex-plots (MTP-specific)	gene-expression-rsem-tpm-collapsed.rds histologies.tsv	Tumor vs normal (GTEx) 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	GitHub	N/A
tumor-normal-differential-expression (MTP-specific)	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	Performs differential expression analysis for all combinations of GTEx subgroup normal and cancer histology type tumor.	No	N/A