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SeqGate

This is the development version of SeqGate; for the stable release version, see SeqGate.

Filtering of Lowly Expressed Features

Bioconductor version: Development (3.18)

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 (from within R, enter citation("SeqGate")):

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 PDF
NEWS Text

Details

biocViews DifferentialExpression, GeneExpression, RNASeq, Sequencing, Software, Transcriptomics
Version 1.11.0
In Bioconductor since BioC 3.12 (R-4.0) (3 years)
License GPL (>= 2.0)
Depends S4Vectors, SummarizedExperiment, GenomicRanges
Imports stats, methods, BiocManager
Linking To
Suggests testthat (>= 3.0.0), edgeR, BiocStyle, knitr, rmarkdown
System Requirements
Enhances
URL
Bug Reports https://github.com/srialle/SeqGate/issues
See More
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package SeqGate_1.11.0.tar.gz
Windows Binary SeqGate_1.11.0.zip
macOS Binary (x86_64) SeqGate_1.11.0.tgz
macOS Binary (arm64) SeqGate_1.11.0.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