SeqGate

DOI: 10.18129/B9.bioc.SeqGate    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see SeqGate.

Filtering of Lowly Expressed Features

Bioconductor version: 3.12

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 "4.0") and enter:

if (!requireNamespace("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")

 

HTML	R Script	SeqGate: Filter lowly expressed features
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, GeneExpression, RNASeq, Sequencing, Software, Transcriptomics
Version	1.0.1
In Bioconductor since	BioC 3.12 (R-4.0) (0.5 years)
License	GPL (>= 2.0)
Depends	S4Vectors, SummarizedExperiment, GenomicRanges
Imports	stats, methods, BiocManager
LinkingTo
Suggests	testthat, 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	SeqGate_1.0.1.tar.gz
Windows Binary	SeqGate_1.0.1.zip
macOS 10.13 (High Sierra)	SeqGate_1.0.1.tgz
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