SeqGate
Filtering of Lowly Expressed Features
Bioconductor version: 3.24 · Package version: 1.23.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
Filtering of lowly expressed features (e.g. genes) is a common step before performing statistical analysis, but an arbitrary threshold is generally chosen. SeqGate implements a method that rationalize this step by the analysis of the distibution of counts in replicate samples. The gate is the threshold above which sequenced features can be considered as confidently quantified.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SeqGate")Details
| Maintainer | Stéphanie Rialle <stephanie.rialle@mgx.cnrs.fr> |
| Author | Christelle Reynès [aut], Stéphanie Rialle [aut, cre] |
| License | GPL (>= 2.0) |
| Bug Reports | https://github.com/srialle/SeqGate/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DifferentialExpression, GeneExpression, RNASeq, Sequencing, Software, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/SeqGate/ |
Citation
From within R, enter citation("SeqGate"):
Christelle Reynès, Stéphanie Rialle. SeqGate: Filtering of Lowly Expressed Features. doi:10.18129/B9.bioc.SeqGate, R package version 1.23.0, https://bioconductor.org/packages/SeqGate.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | SeqGate_1.23.0.tar.gz |
| Windows binary (x86_64) | SeqGate_1.23.0.zip |
| macOS binary (arm64) | SeqGate_1.23.0.tgz |
| macOS binary (x86_64) | SeqGate_1.23.0.tgz |
Dependencies
Depends: S4Vectors, SummarizedExperiment, GenomicRanges
Imports: stats, methods, BiocManager
Suggests: testthat (>= 3.0.0), edgeR, BiocStyle, knitr, rmarkdown