BioQC

DOI: 10.18129/B9.bioc.BioQC    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see BioQC.

Detect tissue heterogeneity in expression profiles with gene sets

Bioconductor version: 3.15

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 [cre, aut], Laura Badi [aut], Gregor Sturm [aut], Roland Ambs [aut], Iakov Davydov [aut]

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

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	BioQC Algorithm: Speeding up the Wilcoxon-Mann-Whitney Test
HTML	R Script	BioQC-benchmark: Testing Efficiency, Sensitivity and Specificity of BioQC on simulated and real-world data
HTML	R Script	BioQC-kidney: The kidney expression example
HTML	R Script	BioQC: Detect tissue heterogeneity in gene expression data
HTML	R Script	Comparing the Wilcoxon-Mann-Whitney to alternative statistical tests
HTML	R Script	Using BioQC with signed genesets
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	GeneExpression, GeneSetEnrichment, QualityControl, Software, StatisticalMethod
Version	1.24.0
In Bioconductor since	BioC 3.3 (R-3.3) (6.5 years)
License	GPL (>=3) + file LICENSE
Depends	R (>= 3.5.0), Biobase
Imports	edgeR, Rcpp, methods, stats, utils
LinkingTo	Rcpp
Suggests	testthat, knitr, rmarkdown, lattice, latticeExtra, rbenchmark, gplots, gridExtra, org.Hs.eg.db, hgu133plus2.db, ggplot2, reshape2, plyr, ineq, covr, limma, RColorBrewer
SystemRequirements
Enhances
URL	https://accio.github.io/BioQC
BugReports	https://accio.github.io/BioQC/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	BioQC_1.24.0.tar.gz
Windows Binary	BioQC_1.24.0.zip (64-bit only)
macOS Binary (x86_64)	BioQC_1.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/BioQC
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BioQC
Package Short Url	https://bioconductor.org/packages/BioQC/
Package Downloads Report	Download Stats