Package: RTCGA 1.42.0
Marcin Kosinski
RTCGA: The Cancer Genome Atlas Data Integration
The Cancer Genome Atlas (TCGA) Data Portal provides a platform for researchers to search, download, and analyze data sets generated by TCGA. It contains clinical information, genomic characterization data, and high level sequence analysis of the tumor genomes. The key is to understand genomics to improve cancer care. RTCGA package offers download and integration of the variety and volume of TCGA data using patient barcode key, what enables easier data possession. This may have an benefcial infuence on impact on development of science and improvement of patients' treatment. Furthermore, RTCGA package transforms TCGA data to tidy form which is convenient to use.
Authors:
RTCGA_1.42.0.tar.gz
RTCGA_1.42.0.zip(r-4.7)RTCGA_1.42.0.zip(r-4.6)RTCGA_1.42.0.zip(r-4.5)
RTCGA_1.42.0.tgz(r-4.6-any)RTCGA_1.42.0.tgz(r-4.5-any)
RTCGA_1.42.0.tar.gz(r-4.7-any)RTCGA_1.42.0.tar.gz(r-4.6-any)
RTCGA_1.42.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
RTCGA/json (API)
NEWS
| # Install 'RTCGA' in R: |
| install.packages('RTCGA', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/rtcga/rtcga/issues
immunooncologysoftwaredataimportdatarepresentationpreprocessingrnaseqsurvivaldnamethylationprincipalcomponentvisualization
Last updated from:a11abb98d3 (on RELEASE_3_23). Checks:8 ERROR, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 754 | ||
| linux-devel-x86_64 | ERROR | 798 | ||
| source / vignettes | OK | 791 | ||
| linux-release-x86_64 | ERROR | 884 | ||
| macos-release-arm64 | ERROR | 433 | ||
| macos-oldrel-arm64 | ERROR | 503 | ||
| windows-devel | ERROR | 486 | ||
| windows-release | ERROR | 442 | ||
| windows-oldrel | ERROR | 469 | ||
| wasm-release | OK | 693 |
Exports:boxplotTCGAcheckTCGAconvertPANCAN12convertTCGAdownloadTCGAexpressionsTCGAheatmapTCGAinfoTCGAinstallTCGAkmTCGAmutationsTCGApcaTCGAreadTCGAsurvivalTCGAtheme_RTCGA
Dependencies:abindaskpassassertthatbackportsbase64encbitopsbootbroombslibcachemcarcarDataclicolorspacecommonmarkcorrplotcowplotcpp11curldata.tableDerivdigestdoBydplyrevaluateexactRankTestsfarverfastmapfontawesomeforecastFormulafracdifffsgenericsggplot2ggpubrggrepelggsciggsignifggtextggthemesgluegridExtragridtextgtablehighrhtmltoolshttrisobandjpegjquerylibjsonliteknitrlabelinglatticelifecyclelitedownlme4lmtestmagrittrmarkdownMASSMatrixMatrixModelsmaxstatmemoisemgcvmicrobenchmarkmimeminqamodelrmvtnormnlmenloptrnnetnumDerivopensslpbkrtestpillarpkgconfigpngpolynompurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRCurlRdpackreformulasrlangrmarkdownrstatixrvestS7sassscalesselectrSparseMstringistringrsurvivalsurvminersystibbletidyrtidyselecttimeDatetinytexurcautf8vctrsviridisviridisLitewithrxfunXMLxml2yamlzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| The Caner Genome Atlas data integration | RTCGA-package RTCGA |
| Create Boxplots for TCGA Datasets | boxplotTCGA |
| Information About Datasets from TCGA Project | checkTCGA |
| Convert Data from RTCGA Family to Bioconductor Classes | convertPANCAN12 convertTCGA |
| RTCGA - The Family of R Packages with Data from The Cancer Genome Atlas Study | datasetsTCGA RTCGA.data |
| Download TCGA Data | downloadTCGA |
| Gather Expressions for TCGA Datasets | expressionsTCGA |
| Create Heatmaps for TCGA Datasets | heatmapTCGA |
| Information About Cohorts from TCGA Project | infoTCGA |
| Install Data Packages from RTCGA Family | installTCGA |
| Plot Kaplan-Meier Estimates of Survival Curves for Survival Data | kmTCGA |
| Gather Mutations for TCGA Datasets | mutationsTCGA |
| Plot Two Main Components of Principal Component Analysis | pcaTCGA |
| Read TCGA data to the tidy Format | readTCGA |
| Extract Survival Information from Datasets Included in RTCGA.clinical and RTCGA.clinical.20160128 Packages | survivalTCGA |
| RTCGA Theme for ggplot2 | theme_RTCGA |
