BioQC

This is the released version of BioQC; for the devel version, see BioQC.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3

Detect tissue heterogeneity in expression profiles with gene sets

Bioconductor version: Release (3.23)

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>

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

Jitao David Zhang, Laura Badi, Gregor Sturm, Roland Ambs, Iakov Davydov. BioQC: Detect tissue heterogeneity in expression profiles with gene sets. doi:10.18129/B9.bioc.BioQC, R package version 1.40.0, https://bioconductor.org/packages/BioQC.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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 Algorithm: 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
BioQC-benchmark: Testing Efficiency, Sensitivity and Specificity of BioQC on simulated and real-world data	HTML	R Script
Comparing the Wilcoxon-Mann-Whitney to alternative statistical tests	HTML	R Script
BioQC-kidney: The kidney expression example	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneExpression, GeneSetEnrichment, QualityControl, Software, StatisticalMethod
Version	1.40.0
In Bioconductor since	BioC 3.3 (R-3.3) (10.5 years)
License	GPL (>=3) + file LICENSE
Depends	R (>= 3.5.0), Biobase
Imports	edgeR, Rcpp, methods, stats, utils
System Requirements
URL	https://accio.github.io/BioQC
Bug Reports	https://accio.github.io/BioQC/issues

Suggests	testthat, knitr, rmarkdown, lattice, latticeExtra, rbenchmark, gplots, gridExtra, org.Hs.eg.db, hgu133plus2.db, ggplot2, reshape2, plyr, ineq, covr, limma, RColorBrewer
Linking To	Rcpp
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	BioQC_1.40.0.tar.gz
Windows Binary (x86_64)	BioQC_1.40.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	BioQC_1.40.0.tgz
macOS Binary (sonoma-arm64)	BioQC_1.40.0.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