RTCGA package | How to download RNAseq data to gain the same datasets as in RTCGA.rnaseq package? | Available cohorts | Downloading RNAseq files | Reading downloaded RNAseq dataset | Shortening paths and directories | Removing NA files from data2 folder | Paths to RNAseq data | Reading RNAseq data using readTCGA | Saving RNAseq data to RTCGA.rnaseq package
Package: RTCGA.rnaseq 20151101.42.0
Marcin Kosinski
RTCGA.rnaseq: Rna-seq datasets from The Cancer Genome Atlas Project
Package provides rna-seq datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Rna-seq data format is explained here https://wiki.nci.nih.gov/display/TCGA/RNASeq+Version+2. Data source is illumina hiseq Level 3 RSEM normalized expression data. Data from 2015-11-01 snapshot.
Authors:
RTCGA.rnaseq_20151101.42.0.tar.gz
RTCGA.rnaseq_20151101.42.0.tar.gz(r-4.7-any)RTCGA.rnaseq_20151101.42.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RTCGA.rnaseq/json (API)
| # Install 'RTCGA.rnaseq' in R: |
| install.packages('RTCGA.rnaseq', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/rtcga/rtcga/issues
Datasets:
- ACC.rnaseq - Rnaseq datasets from TCGA project
- BLCA.rnaseq - Rnaseq datasets from TCGA project
- BRCA.rnaseq - Rnaseq datasets from TCGA project
- CESC.rnaseq - Rnaseq datasets from TCGA project
- CHOL.rnaseq - Rnaseq datasets from TCGA project
- COAD.rnaseq - Rnaseq datasets from TCGA project
- COADREAD.rnaseq - Rnaseq datasets from TCGA project
- DLBC.rnaseq - Rnaseq datasets from TCGA project
- ESCA.rnaseq - Rnaseq datasets from TCGA project
- GBM.rnaseq - Rnaseq datasets from TCGA project
- GBMLGG.rnaseq - Rnaseq datasets from TCGA project
- HNSC.rnaseq - Rnaseq datasets from TCGA project
- KICH.rnaseq - Rnaseq datasets from TCGA project
- KIPAN.rnaseq - Rnaseq datasets from TCGA project
- KIRC.rnaseq - Rnaseq datasets from TCGA project
- KIRP.rnaseq - Rnaseq datasets from TCGA project
- LAML.rnaseq - Rnaseq datasets from TCGA project
- LGG.rnaseq - Rnaseq datasets from TCGA project
- LIHC.rnaseq - Rnaseq datasets from TCGA project
- LUAD.rnaseq - Rnaseq datasets from TCGA project
- LUSC.rnaseq - Rnaseq datasets from TCGA project
- OV.rnaseq - Rnaseq datasets from TCGA project
- PAAD.rnaseq - Rnaseq datasets from TCGA project
- PCPG.rnaseq - Rnaseq datasets from TCGA project
- PRAD.rnaseq - Rnaseq datasets from TCGA project
- READ.rnaseq - Rnaseq datasets from TCGA project
- SARC.rnaseq - Rnaseq datasets from TCGA project
- SKCM.rnaseq - Rnaseq datasets from TCGA project
- STAD.rnaseq - Rnaseq datasets from TCGA project
- STES.rnaseq - Rnaseq datasets from TCGA project
- TGCT.rnaseq - Rnaseq datasets from TCGA project
- THCA.rnaseq - Rnaseq datasets from TCGA project
- THYM.rnaseq - Rnaseq datasets from TCGA project
- UCEC.rnaseq - Rnaseq datasets from TCGA project
- UCS.rnaseq - Rnaseq datasets from TCGA project
- UVM.rnaseq - Rnaseq datasets from TCGA project
On BioConductor:RTCGA.rnaseq-20151101.41.0(data/experiment 3.24)RTCGA.rnaseq-20151101.42.0(data/experiment 3.23)
Last updated from:b660b0a632 (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 | 353 | ||
| linux-devel | WARNING | 514 | ||
| source / vignettes | OK | 2094 | ||
| linux-release | WARNING | 533 |
Exports:
Dependencies:abindaskpassassertthatbackportsbase64encbitopsbootbroombslibcachemcarcarDataclicolorspacecommonmarkcorrplotcowplotcpp11curldata.tableDerivdigestdoBydplyrevaluateexactRankTestsfarverfastmapfontawesomeforecastFormulafracdifffsgenericsggplot2ggpubrggrepelggsciggsignifggtextggthemesgluegridExtragridtextgtablehighrhtmltoolshttrisobandjpegjquerylibjsonliteknitrlabelinglatticelifecyclelitedownlme4lmtestmagrittrmarkdownMASSMatrixMatrixModelsmaxstatmemoisemgcvmimeminqamodelrmvtnormnlmenloptrnnetnumDerivopensslpbkrtestpillarpkgconfigpngpolynompurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRCurlRdpackreformulasrlangrmarkdownrstatixRTCGArvestS7sassscalesselectrSparseMstringistringrsurvivalsurvminersystibbletidyrtidyselecttimeDatetinytexurcautf8vctrsviridisviridisLitewithrxfunXMLxml2yamlzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| rnaseq datasets from TCGA project | ACC.rnaseq ACC.rnaseq,BLCA.rnaseq,BRCA.rnaseq,CESC.rnaseq,CHOL.rnaseq,COAD.rnaseq,COADREAD.rnaseq,DLBC.rnaseq,ESCA.rnaseq,GBMLGG.rnaseq, BLCA.rnaseq BRCA.rnaseq CESC.rnaseq CHOL.rnaseq COAD.rnaseq COADREAD.rnaseq DLBC.rnaseq ESCA.rnaseq GBM.rnaseq GBM.rnaseq,HNSC.rnaseq,KICH.rnaseq,KIPAN.rnaseq,KIRC.rnaseq,KIRP.rnaseq,LAML.rnaseq,LGG.rnaseq,LIHC.rnaseq,LUAD.rnaseq,LUSC.rnaseq,OV.rnaseq,PAAD.rnaseq,PCPG.rnaseq,PRAD.rnaseq,READ.rnaseq,SARC.rnaseq,SKCM.rnaseq,STAD.rnaseq,STES.rnaseq,TGCT.rnaseq,THCA.rnaseq,THYM.rnaseq,UCEC.rnaseq,UCS.rnaseq,UVM.rnaseq GBMLGG.rnaseq HNSC.rnaseq KICH.rnaseq KIPAN.rnaseq KIRC.rnaseq KIRP.rnaseq LAML.rnaseq LGG.rnaseq LIHC.rnaseq LUAD.rnaseq LUSC.rnaseq OV.rnaseq PAAD.rnaseq PCPG.rnaseq PRAD.rnaseq READ.rnaseq rnaseq SARC.rnaseq SKCM.rnaseq STAD.rnaseq STES.rnaseq TGCT.rnaseq THCA.rnaseq THYM.rnaseq UCEC.rnaseq UCS.rnaseq UVM.rnaseq |