BioQC
This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see BioQC.
Detect tissue heterogeneity in expression profiles with gene sets
Bioconductor version: 3.14
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 "4.1") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneExpression, GeneSetEnrichment, QualityControl, Software, StatisticalMethod |
| Version | 1.22.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8 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_1.22.0.tar.gz |
| Windows Binary | BioQC_1.22.0.zip (32- & 64-bit) |
| macOS 10.13 (High Sierra) | BioQC_1.22.0.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 |
| Old Source Packages for BioC 3.14 | Source Archive |