RTCGA package | How to download clinical data to gain the same datasets as in RTCGA.clinical package? | Available cohorts | Downloading clinical files | Reading downloaded clinical dataset | Shortening paths and directories | Removing NA files from data2 folder | Paths to clinical data | Reading clinical data using readTCGA | Saving clinical data to RTCGA.clinical package
Package: RTCGA.clinical 20151101.42.0
Marcin Kosinski
RTCGA.clinical: Clinical datasets from The Cancer Genome Atlas Project
Package provides clinical datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Clinical data format is explained here https://wiki.nci.nih.gov/display/TCGA/Clinical+Data+Overview. Data from 2015-11-01 snapshot.
Authors:
RTCGA.clinical_20151101.42.0.tar.gz
RTCGA.clinical_20151101.42.0.tar.gz(r-4.7-any)RTCGA.clinical_20151101.42.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RTCGA.clinical/json (API)
| # Install 'RTCGA.clinical' in R: |
| install.packages('RTCGA.clinical', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/rtcga/rtcga/issues
Datasets:
- ACC.clinical - Clinical datasets from TCGA project
- BLCA.clinical - Clinical datasets from TCGA project
- BRCA.clinical - Clinical datasets from TCGA project
- CESC.clinical - Clinical datasets from TCGA project
- CHOL.clinical - Clinical datasets from TCGA project
- COAD.clinical - Clinical datasets from TCGA project
- COADREAD.clinical - Clinical datasets from TCGA project
- DLBC.clinical - Clinical datasets from TCGA project
- ESCA.clinical - Clinical datasets from TCGA project
- FPPP.clinical - Clinical datasets from TCGA project
- GBM.clinical - Clinical datasets from TCGA project
- GBMLGG.clinical - Clinical datasets from TCGA project
- HNSC.clinical - Clinical datasets from TCGA project
- KICH.clinical - Clinical datasets from TCGA project
- KIPAN.clinical - Clinical datasets from TCGA project
- KIRC.clinical - Clinical datasets from TCGA project
- KIRP.clinical - Clinical datasets from TCGA project
- LAML.clinical - Clinical datasets from TCGA project
- LGG.clinical - Clinical datasets from TCGA project
- LIHC.clinical - Clinical datasets from TCGA project
- LUAD.clinical - Clinical datasets from TCGA project
- LUSC.clinical - Clinical datasets from TCGA project
- MESO.clinical - Clinical datasets from TCGA project
- OV.clinical - Clinical datasets from TCGA project
- PAAD.clinical - Clinical datasets from TCGA project
- PCPG.clinical - Clinical datasets from TCGA project
- PRAD.clinical - Clinical datasets from TCGA project
- READ.clinical - Clinical datasets from TCGA project
- SARC.clinical - Clinical datasets from TCGA project
- SKCM.clinical - Clinical datasets from TCGA project
- STAD.clinical - Clinical datasets from TCGA project
- STES.clinical - Clinical datasets from TCGA project
- TGCT.clinical - Clinical datasets from TCGA project
- THCA.clinical - Clinical datasets from TCGA project
- THYM.clinical - Clinical datasets from TCGA project
- UCEC.clinical - Clinical datasets from TCGA project
- UCS.clinical - Clinical datasets from TCGA project
- UVM.clinical - Clinical datasets from TCGA project
On BioConductor:RTCGA.clinical-20151101.41.0(data/experiment 3.24)RTCGA.clinical-20151101.42.0(data/experiment 3.23)
Last updated from:2089118450 (on RELEASE_3_23). Checks:1 ERROR, 2 WARNING, 1 OK. Indexed: no.
This is a data package. Data packages may be large and do not get checked across all platforms.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 172 | ||
| linux-devel | WARNING | 269 | ||
| source / vignettes | OK | 339 | ||
| linux-release | WARNING | 253 |
Exports:
Dependencies:abindaskpassassertthatbackportsbase64encbitopsbootbroombslibcachemcarcarDataclicolorspacecommonmarkcorrplotcowplotcpp11curldata.tableDerivdigestdoBydplyrevaluateexactRankTestsfarverfastmapfontawesomeforecastFormulafracdifffsgenericsggplot2ggpubrggrepelggsciggsignifggtextggthemesgluegridExtragridtextgtablehighrhtmltoolshttrisobandjpegjquerylibjsonliteknitrlabelinglatticelifecyclelitedownlme4lmtestmagrittrmarkdownMASSMatrixMatrixModelsmaxstatmemoisemgcvmimeminqamodelrmvtnormnlmenloptrnnetnumDerivopensslpbkrtestpillarpkgconfigpngpolynompurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRCurlRdpackreformulasrlangrmarkdownrstatixRTCGArvestS7sassscalesselectrSparseMstringistringrsurvivalsurvminersystibbletidyrtidyselecttimeDatetinytexurcautf8vctrsviridisviridisLitewithrxfunXMLxml2yamlzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Clinical datasets from TCGA project | ACC.clinical ACC.clinical,BLCA.clinical,BRCA.clinical,CESC.clinical,CHOL.clinical,COAD.clinical,COADREAD.clinical,DLBC.clinical,ESCA.clinical,FPPP.clinical,GBM.clinical,GBMLGG.clinical,HNSC.clinical,KICH.clinical,KIPAN.clinical,KIRC.clinical,KIRP.clinical,LAML.clinical,LGG.clinical,LIHC.clinical,LUAD.clinical,LUSC.clinical,MESO.clinical,OV.clinical,PAAD.clinical,PCPG.clinical,PRAD.clinical,READ.clinical,SARC.clinical,SKCM.clinical,STAD.clinical,STES.clinical,TGCT.clinical,THCA.clinical,THYM.clinical,UCEC.clinical,UCS.clinical,UVM.clinical BLCA.clinical BRCA.clinical CESC.clinical CHOL.clinical clinical COAD.clinical COADREAD.clinical DLBC.clinical ESCA.clinical FPPP.clinical GBM.clinical GBMLGG.clinical HNSC.clinical KICH.clinical KIPAN.clinical KIRC.clinical KIRP.clinical LAML.clinical LGG.clinical LIHC.clinical LUAD.clinical LUSC.clinical MESO.clinical OV.clinical PAAD.clinical PCPG.clinical PRAD.clinical READ.clinical SARC.clinical SKCM.clinical STAD.clinical STES.clinical TGCT.clinical THCA.clinical THYM.clinical UCEC.clinical UCS.clinical UVM.clinical |