estimate: Estimate of Stromal and Immune Cells in Malignant Tumor Tissues from Expression Data

Predicts tumor purity, and the presence of stromal/immune cells in tumor tissues using gene expression data.

Author
Kosuke Yoshihara, Hoon Kim, Roel GW Verhaak
Date of publication
2016-10-04 21:13:08
Maintainer
Kosuke Yoshihara <kyoshihara@mdanderson.org>
License
GPL-2
Version
1.0.13
URLs

View on R-Forge

Man pages

e00-estimate-package
ESTIMATE
e50-estimateScore
Calculation of stromal, immune, and ESTIMATE scores
e50-filterCommonGenes
Intersect input data with 10,412 common genes
e50-outputGCT
Write gene expression data in GCT format
e50-plotPurity
Plot tumor purity
e90-common_genes-data
10,412 common genes
e90-PurityDataAffy-data
Affymetrix data
e90-SI_geneset-data
two signatures for estimate

Files in this package

estimate/DESCRIPTION
estimate/NAMESPACE
estimate/R
estimate/R/estimateScore.R
estimate/R/filterCommonGenes.R
estimate/R/outputGCT.R
estimate/R/plotPurity.R
estimate/R/zzz.R
estimate/build
estimate/build/estimate.pdf
estimate/build/vignette.rds
estimate/data
estimate/data/PurityDataAffy.RData
estimate/data/SI_geneset.RData
estimate/data/common_genes.RData
estimate/inst
estimate/inst/COPYRIGHTS
estimate/inst/NEWS.Rd
estimate/inst/doc
estimate/inst/doc/ESTIMATE_Vignette.R
estimate/inst/doc/ESTIMATE_Vignette.Rnw
estimate/inst/doc/ESTIMATE_Vignette.pdf
estimate/inst/extdata
estimate/inst/extdata/PurityDataAffy.txt
estimate/inst/extdata/SI_geneset.gmt
estimate/inst/extdata/common_genes.txt
estimate/inst/extdata/sample_estimate.gct
estimate/inst/extdata/sample_input.gct
estimate/inst/extdata/sample_input.txt
estimate/inst/extdata/sample_purity.gct
estimate/inst/util
estimate/inst/util/makeData.R
estimate/man
estimate/man/e00-estimate-package.Rd
estimate/man/e50-estimateScore.Rd
estimate/man/e50-filterCommonGenes.Rd
estimate/man/e50-outputGCT.Rd
estimate/man/e50-plotPurity.Rd
estimate/man/e90-PurityDataAffy-data.Rd
estimate/man/e90-SI_geneset-data.Rd
estimate/man/e90-common_genes-data.Rd
estimate/vignettes
estimate/vignettes/ESTIMATE_Vignette.Rnw