BioQC
This is the development version of BioQC; for the stable release version, see BioQC.
Detect tissue heterogeneity in expression profiles with gene sets
Bioconductor version: Development (3.20)
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("BioQC")
):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | GeneExpression, GeneSetEnrichment, QualityControl, Software, StatisticalMethod |
Version | 1.33.0 |
In Bioconductor since | BioC 3.3 (R-3.3) (8.5 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 |
See More
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 |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | BioQC_1.33.0.tar.gz |
Windows Binary | BioQC_1.33.0.zip (64-bit only) |
macOS Binary (x86_64) | BioQC_1.33.0.tgz |
macOS Binary (arm64) | BioQC_1.33.0.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 |