SeqGate
This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see SeqGate.
Filtering of Lowly Expressed Features
Bioconductor version: 3.13
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.
Author: Christelle Reynès [aut], Stéphanie Rialle [aut, cre]
Maintainer: Stéphanie Rialle <stephanie.rialle at mgx.cnrs.fr>
citation("SeqGate")):
Installation
To install this package, start R (version "4.1") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SeqGate")
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("SeqGate")| SeqGate: Filter lowly expressed features | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, RNASeq, Sequencing, Software, Transcriptomics |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (3.5 years) |
| License | GPL (>= 2.0) |
| Depends | S4Vectors, SummarizedExperiment, GenomicRanges |
| Imports | stats, methods, BiocManager |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/srialle/SeqGate/issues |
See More
| Suggests | testthat (>= 3.0.0), edgeR, BiocStyle, knitr, rmarkdown |
| Linking To | |
| 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 | SeqGate_1.2.0.tar.gz |
| Windows Binary | SeqGate_1.2.0.zip |
| macOS 10.13 (High Sierra) | SeqGate_1.2.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SeqGate |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SeqGate |
| Bioc Package Browser | https://code.bioconductor.org/browse/SeqGate/ |
| Package Short Url | https://bioconductor.org/packages/SeqGate/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.13 | Source Archive |