This directory contains various analysis modules in the OpenPedCan project. See the README of an individual analysis modules for more information about that module.
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 |
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| 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](https://github.com/d3b-center/OpenPedCan-analysis/blob/dev/analyses/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](https://github.com/d3b-center/OpenPedCan-analysis/blob/dev/analyses/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](https://github.com/d3b-center/OpenPedCan-analysis/blob/dev/analyses/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](https://github.com/d3b-center/OpenPedCan-analysis/blob/dev/analyses/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](https://github.com/d3b-center/OpenPedCan-analysis/blob/dev/analyses/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.gz included 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 | | | | | Yes | Yes | HPC CAVATICA user can create application for personal analysis purpose using scripts provided in the module | N/A |