Package: terraTCGAdata 1.11.0

terraTCGAdata: OpenAccess TCGA Data on Terra as MultiAssayExperiment

Leverage the existing open access TCGA data on Terra with well-established Bioconductor infrastructure. Make use of the Terra data model without learning its complexities. With a few functions, you can copy / download and generate a MultiAssayExperiment from the TCGA example workspaces provided by Terra.

Authors:Marcel Ramos [aut, cre]

terraTCGAdata_1.11.0.tar.gz
terraTCGAdata_1.11.0.zip(r-4.5)terraTCGAdata_1.11.0.zip(r-4.4)terraTCGAdata_1.11.0.zip(r-4.3)
terraTCGAdata_1.11.0.tgz(r-4.4-any)terraTCGAdata_1.9.2.tgz(r-4.3-any)
terraTCGAdata_1.11.0.tar.gz(r-4.5-noble)terraTCGAdata_1.11.0.tar.gz(r-4.4-noble)
terraTCGAdata_1.11.0.tgz(r-4.4-emscripten)terraTCGAdata_1.11.0.tgz(r-4.3-emscripten)
terraTCGAdata.pdf |terraTCGAdata.html✨
terraTCGAdata/json (API)
NEWS

# Install 'terraTCGAdata' in R:

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

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

On BioConductor:terraTCGAdata-1.9.2(bioc 3.20)terraTCGAdata-1.8.0(bioc 3.19)

software infrastructure dataimport bioconductor-package

4.60 score 4 scripts 9 exports 133 dependencies

Last updated 23 days agofrom:3e2116729e. Checks:OK: 7. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	OK	Oct 31 2024
R-4.5-linux	OK	Oct 30 2024
R-4.4-win	OK	Oct 31 2024
R-4.4-mac	OK	Oct 31 2024
R-4.3-win	OK	Oct 31 2024
R-4.3-mac	OK	Sep 30 2024

Exports:getAssayData getAssayTable getClinical getClinicalTable getTCGAdatalist sampleTypesTable selectTCGAworkspace terraTCGAdata terraTCGAworkspace

Dependencies:abind AnnotationDbi AnVIL AnVILBase AnVILGCP askpass base64enc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel Biostrings bit bit64 bitops blob bslib cachem cli clipr codetools commonmark cpp11 crayon crosstalk curl DBI dbplyr DelayedArray digest dplyr DT evaluate fansi fastmap filelock fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicDataCommons GenomicFeatures GenomicRanges glue highr hms htmltools htmlwidgets httpuv httr httr2 IRanges jquerylib jsonlite KEGGREST knitr lambda.r later lattice lazyeval lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime miniUI MultiAssayExperiment openssl pillar pkgconfig plogr png prettyunits progress promises purrr R6 RaggedExperiment rapiclient rappdirs Rcpp RCurl readr restfulr Rhtslib rjson rlang rmarkdown Rsamtools RSQLite rtracklayer rvest S4Arrays S4Vectors sass selectr shiny snow sourcetools SparseArray stringi stringr SummarizedExperiment sys TCGAutils tibble tidyr tidyselect tinytex tzdb UCSC.utils utf8 vctrs vroom withr xfun XML xml2 xtable XVector yaml zlibbioc

terraTCGAdata Introduction

Marcel Ramos

Rendered fromterraTCGAdata.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2024-09-30
Started: 2022-01-12

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Obtain assay datasets from Terra	getAssayData
Obtain a reference table for assay data in the Terra data model	getAssayTable
Obtain clinical data	getClinical
Obtain the reference table for clinical data	getClinicalTable
Import Terra TCGA data as a list	getTCGAdatalist
Get an overview of the samples available in the workspace	sampleTypesTable
Obtain a MultiAssayExperiment from the Terra workspace	terraTCGAdata
Obtain or set the Terra Workspace Project Dataset	selectTCGAworkspace terraTCGAworkspace