Package: TCGAutils 1.27.0

TCGAutils: TCGA utility functions for data management

A suite of helper functions for checking and manipulating TCGA data including data obtained from the curatedTCGAData experiment package. These functions aim to simplify and make working with TCGA data more manageable. Exported functions include those that import data from flat files into Bioconductor objects, convert row annotations, and identifier translation via the GDC API.

Authors:Marcel Ramos [aut, cre], Lucas Schiffer [aut], Sean Davis [ctb], Levi Waldron [aut]

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TCGAutils.pdf |TCGAutils.html✨
TCGAutils/json (API)
NEWS

# Install 'TCGAutils' in R:

install.packages('TCGAutils', repos = c('https://link-ny.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/waldronlab/tcgautils/issues

Datasets:

clinicalNames - Clinical dataset names in TCGA
diseaseCodes - TCGA Cancer Disease Codes Table
sampleTypes - Barcode Sample Type Table

On BioConductor:TCGAutils-1.27.0(bioc 3.21)TCGAutils-1.26.0(bioc 3.20)

software workflowstep preprocessing dataimport bioconductor-package tcga utilities

9.37 score 23 stars 8 packages 204 scripts 32 exports 96 dependencies

Last updated 21 days agofrom:e8f6f5396f. Checks:OK: 1 NOTE: 5 ERROR: 1. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Nov 19 2024
R-4.5-win	NOTE	Nov 19 2024
R-4.5-linux	NOTE	Nov 19 2024
R-4.4-win	NOTE	Nov 19 2024
R-4.4-mac	NOTE	Nov 19 2024
R-4.3-win	NOTE	Nov 19 2024
R-4.3-mac	ERROR	Oct 21 2024

Exports:barcodeToUUID correctBuild CpGtoRanges extractBuild filenameToBarcode findGRangesCols generateMap getClinicalNames getFileName getSubtypeMap imputeAssay isCorrect makeGRangesListFromCopyNumber makeGRangesListFromExonFiles mergeColData mirToRanges oncoPrintTCGA qreduceTCGA sampleTables simplifyTCGA symbolsToRanges TCGAbarcode TCGAbiospec TCGAprimaryTumors TCGAsampleSelect TCGAsplitAssays translateBuild trimColData uniformBuilds UUIDhistory UUIDtoBarcode UUIDtoUUID

Dependencies:abind AnnotationDbi askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob cachem cli clipr codetools cpp11 crayon curl DBI DelayedArray dplyr fansi fastmap formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicDataCommons GenomicFeatures GenomicRanges glue hms httr IRanges jsonlite KEGGREST lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime MultiAssayExperiment openssl pillar pkgconfig plogr png prettyunits progress purrr R6 RaggedExperiment rappdirs RCurl readr restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer rvest S4Arrays S4Vectors selectr snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tzdb UCSC.utils utf8 vctrs vroom withr XML xml2 XVector yaml zlibbioc

TCGAutils: Helper functions for working with TCGA datasets

Marcel Ramos & Levi Waldron

Rendered fromTCGAutils.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2023-10-17
Started: 2017-12-21

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
TCGAutils: Helper functions for working with TCGA and MultiAssayExperiment data	TCGAutils-package TCGAutils
Utilities for working with _HUMAN_ genome builds	builds correctBuild extractBuild isCorrect translateBuild uniformBuilds
Clinical dataset names in TCGA	clinicalNames
Helper functions for managing MultiAssayExperiment from curatedTCGAData	curatedTCGAData-helpers getClinicalNames getSubtypeMap sampleTables TCGAsplitAssays
TCGA Cancer Disease Codes Table	diseaseCodes
Obtain minimum necessary names for the creation of a GRangesList object	findGRangesCols
Create a sampleMap from an experiment list and phenoData dataframe	generateMap
Find the file names used in RTCGAToolbox	getFileName
Translate study identifiers from barcode to UUID and vice versa	barcodeToUUID filenameToBarcode ID-translation UUIDhistory UUIDtoBarcode UUIDtoUUID
This function imputes assays values inside a 'MultiAssayExperiment'	imputeAssay
Make a GRangesList from TCGA Copy Number data	makeGRangesListFromCopyNumber
Read exon-level expression files and create a 'GRangesList'	makeGRangesListFromExonFiles
Take a MultiAssayExperiment and include curated variables	mergeColData
OncoPrint for TCGA Mutation Assays	oncoPrintTCGA
Barcode Sample Type Table	sampleTypes
Functions to convert rows annotations to ranges and RaggedExperiment to RangedSummarizedExperiment	CpGtoRanges mirToRanges qreduceTCGA simplifyTCGA symbolsToRanges
Parse data from TCGA barcode	TCGAbarcode
Extract biospecimen data from the TCGA barcode	TCGAbiospec
Select primary tumors from TCGA datasets	TCGAprimaryTumors
Select samples from barcodes from lookup table	TCGAsampleSelect
Minimize the number of variables in colData	trimColData