estimate: Estimate of Stromal and Immune Cells in Malignant Tumor Tissues from Expression Data
Version 1.0.13

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

AuthorKosuke Yoshihara, Hoon Kim, Roel GW Verhaak
Date of publication2016-10-04 21:13:08
MaintainerKosuke Yoshihara <kyoshihara@mdanderson.org>
LicenseGPL-2
Version1.0.13
URL https://r-forge.r-project.org/projects/estimate/
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("estimate", repos="http://R-Forge.R-project.org")

Popular man pages

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
See all...

All man pages Function index File listing

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

Functions

PurityDataAffy Man page
SI_geneset Man page
common_genes Man page
estimate Man page
estimate-package Man page
estimateScore Man page Source code
filterCommonGenes Man page Source code
onAttach Source code
onLoad Source code
outputGCT Man page Source code
plotPurity Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/estimateScore.R
R/filterCommonGenes.R
R/outputGCT.R
R/plotPurity.R
R/zzz.R
build
build/estimate.pdf
build/vignette.rds
data
data/PurityDataAffy.RData
data/SI_geneset.RData
data/common_genes.RData
inst
inst/COPYRIGHTS
inst/NEWS.Rd
inst/doc
inst/doc/ESTIMATE_Vignette.R
inst/doc/ESTIMATE_Vignette.Rnw
inst/doc/ESTIMATE_Vignette.pdf
inst/extdata
inst/extdata/PurityDataAffy.txt
inst/extdata/SI_geneset.gmt
inst/extdata/common_genes.txt
inst/extdata/sample_estimate.gct
inst/extdata/sample_input.gct
inst/extdata/sample_input.txt
inst/extdata/sample_purity.gct
inst/util
inst/util/makeData.R
man
man/e00-estimate-package.Rd
man/e50-estimateScore.Rd
man/e50-filterCommonGenes.Rd
man/e50-outputGCT.Rd
man/e50-plotPurity.Rd
man/e90-PurityDataAffy-data.Rd
man/e90-SI_geneset-data.Rd
man/e90-common_genes-data.Rd
vignettes
vignettes/ESTIMATE_Vignette.Rnw
estimate documentation built on May 21, 2017, 12:19 a.m.

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