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 (3.17)

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>

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

PDF		Reference Manual

Details

biocViews	DifferentialExpression, GeneExpression, RNASeq, Sequencing, Software, Transcriptomics
Version	1.9.0
In Bioconductor since	BioC 3.12 (R-4.0) (2 years)
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
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Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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/
Package Downloads Report	Download Stats