BioQC
This is the released version of BioQC; for the devel version, see BioQC.
Detect tissue heterogeneity in expression profiles with gene sets
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 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 | 1.40.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (10.5 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_1.40.0.tar.gz |
| Windows Binary (x86_64) | BioQC_1.40.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | BioQC_1.40.0.tgz |
| macOS Binary (sonoma-arm64) | BioQC_1.40.0.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 |