BioQC: Detect tissue heterogeneity in expression profiles with gene sets
Version 1.4.0

BioQC performs quality control of high-throughput expression data based on tissue gene signatures

AuthorJitao David Zhang <jitao_david.zhang@roche.com>, with inputs from Laura Badi
Bioconductor views GeneExpression QualityControl StatisticalMethod
Date of publicationNone
MaintainerJitao David Zhang <jitao_david.zhang@roche.com>
LicenseLGPL (>=2)
Version1.4.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("BioQC")

Popular man pages

absLog10p: Absolute base-10 logarithm of p-values
entropy: Shannon entropy and related concepts
filterPmat: Filter rows of p-value matrix under the significance...
gini: Calculate Gini Index of a numeric vector
readGmt: Read in gene sets from a GMT file
wmwTest: Wilcoxon-Mann-Whitney rank sum test for high-throughput...
See all...

All man pages Function index File listing

Man pages

absLog10p: Absolute base-10 logarithm of p-values
entropy: Shannon entropy and related concepts
filterPmat: Filter rows of p-value matrix under the significance...
gini: Calculate Gini Index of a numeric vector
readGmt: Read in gene sets from a GMT file
wmwTest: Wilcoxon-Mann-Whitney rank sum test for high-throughput...

Functions

absLog10p Man page Source code
atomDiversity Source code
atomEntropy Source code
entropy Man page Source code
entropyDiversity Man page Source code
entropySpecificity Man page Source code
filterPmat Man page Source code
gini Man page Source code
rankSumTestWithCorrelation Source code
readGmt Man page Source code
sampleSpecialization Man page Source code
wmw.test Source code
wmwTest Man page Source code

Files

DESCRIPTION
Makefile
NAMESPACE
NEWS
R
R/entropy.R
R/gini.R
R/readGmt.R
R/utils.R
R/wmw-ranksum-Zar.R
R/wmwTest.R
build
build/vignette.rds
inst
inst/Rscript
inst/Rscript/bioqc.Rscript
inst/doc
inst/doc/bioqc.R
inst/doc/bioqc.Rnw
inst/doc/bioqc.pdf
inst/extdata
inst/extdata/exp.tissuemark.affy.roche.symbols.gmt
inst/extdata/test.gct
man
man/absLog10p.Rd
man/entropy.Rd
man/filterPmat.Rd
man/gini.Rd
man/readGmt.Rd
man/wmwTest.Rd
src
src/Makevars
src/bioqc.c
src/bioqc.h
src/gini.c
src/read_gmt.cpp
src/read_gmt.h
src/stat_rank.c
src/stat_rank.h
src/wmw_test_R.c
tests
tests/testthat
tests/testthat.R
tests/testthat/test-wmwTest.R
vignettes
vignettes/bioqc.Rnw
BioQC documentation built on May 20, 2017, 10:12 p.m.

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