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 | chromothripsis analysis per #1007 | 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 (DEPRECATED) | 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 | GitHub | N/A |
| collapse-rnaseq (DEPRECATED) | gene-expression-rsem-tpm.rds gencode.v39.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 | CAVATICA | N/A |
| comparative-RNASeq-analysis (DEPRECATED) | 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 | N/A | N/A |
| compare-gistic (DEPRECATED) | 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 | 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/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 continuous integration | 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) (**DEPRECATED**) | 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) (**DEPRECATED**) | 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 | Remove 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 [#186](https://github.com/d3b-center/OpenPedCan-analysis/issues/186) | 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 (DEPRECATED) | 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 | 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 | GitHub | N/A |
| gene_match (DEPRECATED) | 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 | ensg-hugo-pmtl-mapping.tsv | 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 | GitHub | Move to CAVATICA |
| hotspots-detection (DEPRECATED) | 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 | CAVATICA | N/A |
| immune-deconv | gene-expression-rsem-tpm-collapsed.rds data/histologies.tsv | Immune/Stroma characterization across PBTA part of #15 | No | xcell_output.rds quantiseq_output.rds | 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 | 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 | N/A | N/A |
| long-format-table-utils (DEPRECATED) | 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 (DEPRECATED) | 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 | 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 | Cavatica | N/A |
| methylation-summary (DEPRECATED) | 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 | Summarize preprocessed Illumina Infinium Human Methylation array measurements produced by the OpenPedCan methylation preprocessing module and Illumina infinium methylation array CpG probe coordinates. | No | N/A | No | aws | N/A |
| molecular-subtyping-ATRT | histologies-base.tsv | Molecular subtyping of ATRT samples | No | NA | GitHub | 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 | 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 | 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 | 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 | 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 | GitHub | N/A |
| molecular-subtyping-MB | histologies-base.tsv gene-expression-rsem-tpm-collapsed.rds | Molecular classification of Medulloblastoma subtypes part of #116 | No | results/MB_molecular_subtype.tsv | 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 | 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 | 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 | 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 | 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 NBL tumors #417 | 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 Neurocytoma samples #805 | 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 | Compile output from other molecular subtyping modules and incorporate pathology feedback #645 | 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 Pineoblastoma samples PR #476 | No | results/pineo-molecular-subtypes.tsv | Yes | GitHub | N/A |
| mtp-annotations (DEPRECATED) | scratch/mtp-json/targets/ scratch/mtp-json/diseases/ | This module transforms OpenTargetsPlatform 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 (DEPRECATED) | 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 |
| mutect2-vs-strelka2 (DEPRECATED) | 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 | 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 | 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 | 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 | 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 | 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 | Generate and validate an Excel spreadsheet for Pediatric Open Targets PedOT website table display orders and names | No | Upload to FNL BOX | Yes | GitHub | N/A |
| rna-seq-composition (DEPRECATED) | 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 | N/A | N/A |
| rnaseq-batch-correct | gene-counts-rsem-expected_count-collapsed.rds histologies.tsv hk_genes_normals.rds [positive_control_genes].rds | RUVseq-DESeq2 batch-corrected DGE analysis | Yes | N/A | Yes | Github | N/A |
| rna-seq-expression-summary-stats (DEPRECATED) | 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 | 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 |
| sample-distribution-analysis (DEPRECATED) | histologies.tsv | Produces plots and tables that illustrate the distribution of different histologies in the PBTA data | No | N/A | No | N/A | N/A |
| sex-prediction-from-RNASeq (DEPRECATED) | gene-expression-kallisto.stranded.rds histologies.tsv | predicts genetic sex using RNA-seq data #84 | No | N/A | No | N/A | N/A |
| snv-frequencies (DEPRECATED) | 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 | GitHub | N/A |
| survival-analysis | TBD | In progress; will eventually contain functions for various types of survival analysis #18 | No | N/A | 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 | 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 | The Tumor Mutation Burden calculation is adapted from snv-callers module of the OpenPBTA-analyses, but uses the consensus SNV calls from 2/4 Mutect2, Strelka2, Lancet, and Vardict callers. | Yes | snv-mutation-tmb-all.tsv snv-mutation-tmb-coding.tsv | Yes | GitHub | N/A |
| tmb-compare (DEPRECATED) | 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 | 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 | 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 | N/A | N/A |
| tcga-capture-kit-investigation (DEPRECATED) | 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 | No | GitHub | N/A |
| tumor-gtex-plots (DEPRECATED) | 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 | GitHub | N/A |
| tumor-normal-differential-expression (DEPRECATED) | 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 |