BioQC
This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see BioQC.
Detect tissue heterogeneity in expression profiles with gene sets
Bioconductor version: 3.10
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 <jitao_david.zhang at roche.com>, Laura Badi, Gregor Sturm, Roland Ambs
Maintainer: Jitao David Zhang <jitao_david.zhang at roche.com>
citation("BioQC")
):
Installation
To install this package, start R (version "3.6") 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 Alogrithm: 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 |
Reference Manual | ||
NEWS | Text |
Details
biocViews | GeneExpression, GeneSetEnrichment, QualityControl, Software, StatisticalMethod |
Version | 1.14.0 |
In Bioconductor since | BioC 3.3 (R-3.3) (8 years) |
License | GPL (>=3) |
Depends | Biobase |
Imports | edgeR, Rcpp, methods, stats, utils |
System Requirements | |
URL |
See More
Suggests | testthat, knitr, rmarkdown, lattice, latticeExtra, rbenchmark, gplots, gridExtra, org.Hs.eg.db, ineq, covr |
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_1.14.0.tar.gz |
Windows Binary | BioQC_1.14.0.zip (32- & 64-bit) |
Mac OS X 10.11 (El Capitan) | BioQC_1.14.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/BioQC |
Source Repository (Developer Access) | git clone [email protected]:packages/BioQC |
Bioc Package Browser | https://code.bioconductor.org/browse/BioQC/ |
Package Short Url | https://bioconductor.org/packages/BioQC/ |
Package Downloads Report | Download Stats |
Old Source Packages for BioC 3.10 | Source Archive |