BioQC

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see BioQC.

Detect tissue heterogeneity in expression profiles with gene sets

Bioconductor version: 3.21

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")):

Installation

To install this package, start R (version "4.5") 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-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 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 1.36.0

In Bioconductor since BioC 3.3 (R-3.3) (9.5 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

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Package Archives

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

Source Package BioQC_1.36.0.tar.gz

Windows Binary (x86_64) BioQC_1.36.0.zip

macOS Binary (x86_64) BioQC_1.36.0.tgz

macOS Binary (arm64) BioQC_1.36.0.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/

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