SeqGate

DOI: 10.18129/B9.bioc.SeqGate    

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

Filtering of Lowly Expressed Features

Bioconductor version: Development (3.15)

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 <christelle.reynes at igf.cnrs.fr>, Stéphanie Rialle <stephanie.rialle at mgx.cnrs.fr>

Maintainer: Stéphanie Rialle <stephanie.rialle at mgx.cnrs.fr>

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

Installation

To install this package, start R (version "4.2") and enter:

if (!requireNamespace("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

PDF   Reference Manual

Details

biocViews DifferentialExpression, GeneExpression, RNASeq, Sequencing, Software, Transcriptomics
Version 1.5.0
In Bioconductor since BioC 3.12 (R-4.0) (1 year)
License GPL (>= 2.0)
Depends S4Vectors, SummarizedExperiment, GenomicRanges
Imports stats, methods, BiocManager
LinkingTo
Suggests testthat (>= 3.0.0), edgeR, BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL
BugReports https://github.com/srialle/SeqGate/issues
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
Windows Binary
macOS 10.13 (High Sierra)
Source Repository git clone https://git.bioconductor.org/packages/SeqGate
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SeqGate
Package Short Url https://bioconductor.org/packages/SeqGate/
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