RTCGAToolbox: a new tool for exporting TCGA Firehose data.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:25181531", "kind": "science-record", "revision": 8, "content_hash": "sha256:66378912c9dc9c01935a0042f63d7cb648a75166d2d8dab016d9a8c2f20b40bf", "created_at": "2026-11-01T15:40:05Z", "updated_at": "2026-11-01T22:42:06Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "RTCGAToolbox: a new tool for exporting TCGA Firehose data.", "doi": "10.1371/journal.pone.0106397", "pmid": "25181531", "authors": ["Mehmet Kemal Samur"], "journal": "PloS one", "year": 2014, "abstract": "BACKGROUND & OBJECTIVE: Managing data from large-scale projects (such as The Cancer Genome Atlas (TCGA)) for further analysis is an important and time consuming step for research projects. Several efforts, such as the Firehose project, make TCGA pre-processed data publicly available via web services and data portals, but this information must be managed, downloaded and prepared for subsequent steps. We have developed an open source and extensible R based data client for pre-processed data from the Firehouse, and demonstrate its use with sample case studies. Results show that our RTCGAToolbox can facilitate data management for researchers interested in working with TCGA data. The RTCGAToolbox can also be integrated with other analysis pipelines for further data processing.\nAVAILABILITY AND IMPLEMENTATION: The RTCGAToolbox is open-source and licensed under the GNU General Public License Version 2.0. All documentation and source code for RTCGAToolbox is freely available at http://mksamur.github.io/RTCGAToolbox/ for Linux and Mac OS X operating systems.", "claims": [{"id": "claim-method", "statement": "It takes sample barcodes to differentiate between “Normal” and “Tumor” samples, and compares them with linear models and empirical Bayesian methods provided by the limma [20] package.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25181531", "locator": "sections[5] \"RTCGAToolbox Data Client and Analysis Functions\" paragraph 6", "quote": "It takes sample barcodes to differentiate between “Normal” and “Tumor” samples, and compares them with linear models and empirical Bayesian methods provided by the limma [20] package."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The authors confirm that all data underlying the findings are fully available without restriction. All relevant data are within the paper and its Supporting Information files and http://mksamur.github.io/RTCGAToolbox.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25181531", "locator": "sections[10] \"Data Availability\" paragraph 2", "quote": "The authors confirm that all data underlying the findings are fully available without restriction. All relevant data are within the paper and its Supporting Information files and http://mksamur.github.io/RTCGAToolbox."}], "state": "complete"}, {"id": "claim-target-result", "statement": "RTCGAToolbox facilitates management and downstream analysis of TCGA data accessed through the Firehose pre-processed data service, with differential gene-expression analysis implemented using limma linear models, empirical Bayesian methods, and voom.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:25181531", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Results show that our RTCGAToolbox can facilitate data management for researchers interested in working with TCGA data."}, {"asset": "source:pmid:25181531", "locator": "sections[2] \"Implementation\" paragraph 4", "quote": "RTCGAToolbox uses the Firehose project, one of the largest TCGA data sources operated by Broad Institute's Genome Data Analysis Center (GDAC), to access Level 3 (segmented or interpreted data) and Level 4 (region of interest data) pre-processed data."}, {"asset": "source:pmid:25181531", "locator": "sections[2] \"Implementation\" paragraph 5", "quote": "The main module of the RTCGAToolbox accesses reports via HTTP calls, and uses text processing functionalities to prepare required information for subsequent steps."}, {"asset": "source:pmid:25181531", "locator": "sections[5] \"RTCGAToolbox Data Client and Analysis Functions\" paragraph 6", "quote": "The “getDiffExpressedGenes” function provides the results of differential gene expression analysis. It takes sample barcodes to differentiate between “Normal” and “Tumor” samples, and compares them with linear models and empirical Bayesian methods provided by the limma [20] package. It also uses voom [21] function (from the same package) to prepare raw RNAseq counts for differential gene expression analysis."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "RTCGAToolbox facilitates management and downstream analysis of TCGA data accessed through the Firehose pre-processed data service, with differential gene-expression analysis implemented using limma linear models, empirical Bayesian methods, and voom.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:25181531"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4152273", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:25181531:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:43020e4b5de265e6ac067ca953f07273a5863d06bc9835846a2c94b80b2d991e", "bytes": 2245, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#pone-0106397-t001", "version": null, "note": "Current Firehose data content (Some of these data may not be accessible due to TCGA data restrictions, full data table can be accessible via http://gdac.broadinstitute.org/runs/stddata__2014_03_16/ingested_data.html).", "structure": {"pmcid": "PMC4152273", "section_index": 1, "section_title": "Introduction", "row_count": 32, "column_count": 10}, "table": {"label": "Table 1", "caption": "Current Firehose data content (Some of these data may not be accessible due to TCGA data restrictions, full data table can be accessible via http://gdac.broadinstitute.org/runs/stddata__2014_03_16/ingested_data.html).", "rows": [["Cohort", "Clinical", "CN", "Methylation", "mRNA", "mRNASeq", "miR", "miRSeq", "RPPA", "MAF"], ["ACC", "15", "90", "80", "0", "79", "0", "80", "0", "90"], ["BLCA", "198", "252", "242", "0", "241", "0", "241", "127", "130"], ["BRCA", "981", "1041", "1024", "526", "1037", "0", "1021", "408", "976"], ["CESC", "127", "192", "189", "0", "185", "0", "200", "0", "39"], ["COAD", "436", "427", "434", "153", "432", "0", "406", "331", "154"], ["COADREAD", "604", "589", "596", "222", "595", "0", "549", "461", "223"], ["DLBC", "21", "28", "28", "0", "28", "0", "27", "0", "0"], ["ESCA", "39", "97", "93", "0", "0", "0", "72", "0", "0"], ["GBM", "578", "570", "414", "540", "160", "565", "0", "214", "290"], ["HNSC", "408", "509", "457", "0", "497", "0", "512", "212", "306"], ["KICH", "93", "66", "66", "0", "66", "0", "66", "0", "66"], ["KIRC", "507", "514", "511", "72", "518", "0", "502", "454", "417"], ["KIRP", "164", "182", "198", "16", "172", "0", "198", "0", "168"], ["LAML", "200", "197", "194", "0", "179", "0", "188", "0", "197"], ["LGG", "305", "463", "403", "27", "463", "0", "438", "258", "289"], ["LIHC", "151", "190", "194", "0", "191", "0", "200", "0", "0"], ["LUAD", "466", "493", "555", "32", "488", "0", "491", "237", "229"], ["LUSC", "411", "490", "492", "154", "489", "0", "467", "195", "178"], ["MESO", "13", "37", "37", "0", "0", "0", "0", "0", "0"], ["OV", "580", "576", "584", "574", "296", "570", "453", "412", "316"], ["PAAD", "73", "91", "91", "0", "85", "0", "85", "0", "91"], ["PCPG", "10", "0", "179", "0", "0", "0", "0", "0", "0"], ["PRAD", "199", "331", "336", "0", "297", "0", "326", "164", "261"], ["READ", "168", "162", "162", "69", "163", "0", "143", "130", "69"], ["SARC", "102", "137", "170", "0", "103", "0", "136", "0", "0"], ["SKCM", "341", "385", "374", "0", "372", "0", "354", "205", "344"], ["STAD", "311", "352", "373", "0", "274", "0", "323", "264", "221"], ["THCA", "484", "494", "496", "0", "494", "0", "495", "222", "402"], ["UCEC", "482", "525", "532", "54", "527", "0", "513", "200", "248"], ["UCS", "57", "56", "57", "0", "57", "0", "56", "0", "57"], ["Totals", "7920", "8947", "8965", "2217", "7893", "1135", "7993", "4033", "5538"]], "row_count": 32, "column_count": 10, "numeric_cells": 279, "header_rows": 1, "locator": "section[1]/table-wrap[1]#pone-0106397-t001"}}, {"id": "asset:table:pmid:25181531:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:76830d0afd55d9409cd224f84e3ba7ed6af23468ae567ebb5a88b6e153500612", "bytes": 1885, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#pone-0106397-t002", "version": null, "note": "Data types supported by RTCGAToolbox.", "structure": {"pmcid": "PMC4152273", "section_index": 5, "section_title": "RTCGAToolbox Data Client and Analysis Functions", "row_count": 13, "column_count": 3}, "table": {"label": "Table 2", "caption": "Data types supported by RTCGAToolbox.", "rows": [["Data Type (Parameter)", "Description", "Output Object (FirehoseData)"], ["Clinic", "Provides clinical information for each sample. 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