BioQC

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see BioQC.

Detect tissue heterogeneity in expression profiles with gene sets


Bioconductor version: 3.12

BioQC performs quality control of high-throughput expression data based on tissue gene signatures. It can detect tissue heterogeneity in gene expression data. The core algorithm is a Wilcoxon-Mann-Whitney test that is optimised for high performance.

Author: Jitao David Zhang <jitao_david.zhang at roche.com>, Laura Badi, Gregor Sturm, Roland Ambs

Maintainer: Jitao David Zhang <jitao_david.zhang at roche.com>

Citation (from within R, enter citation("BioQC")):

Installation

To install this package, start R (version "4.0") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("BioQC")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("BioQC")
BioQC Alogrithm: Speeding up the Wilcoxon-Mann-Whitney Test HTML R Script
BioQC: Detect tissue heterogeneity in gene expression data HTML R Script
Using BioQC with signed genesets HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneExpression, GeneSetEnrichment, QualityControl, Software, StatisticalMethod
Version 1.18.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License GPL (>=3)
Depends Biobase
Imports edgeR, Rcpp, methods, stats, utils
System Requirements
URL
See More
Suggests testthat, knitr, rmarkdown, lattice, latticeExtra, rbenchmark, gplots, gridExtra, org.Hs.eg.db, ineq, covr
Linking To Rcpp
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package BioQC_1.18.0.tar.gz
Windows Binary BioQC_1.18.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra) BioQC_1.18.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/BioQC
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BioQC
Bioc Package Browser https://code.bioconductor.org/browse/BioQC/
Package Short Url https://bioconductor.org/packages/BioQC/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.12 Source Archive