BioQC

DOI: 10.18129/B9.bioc.BioQC    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see BioQC.

Detect tissue heterogeneity in expression profiles with gene sets

Bioconductor version: 3.13

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 "4.1") and enter:

if (!requireNamespace("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 1.20.0
In Bioconductor since BioC 3.3 (R-3.3) (5.5 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_1.20.0.tar.gz
Windows Binary BioQC_1.20.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra) BioQC_1.20.0.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

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