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Filtering of Lowly Expressed Features

Bioconductor version: Release (3.19)

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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

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


biocViews DifferentialExpression, GeneExpression, RNASeq, Sequencing, Software, Transcriptomics
Version 1.14.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License GPL (>= 2.0)
Depends S4Vectors, SummarizedExperiment, GenomicRanges
Imports stats, methods, BiocManager
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Suggests testthat (>= 3.0.0), edgeR, BiocStyle, knitr, rmarkdown
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Follow Installation instructions to use this package in your R session.

Source Package SeqGate_1.14.0.tar.gz
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macOS Binary (arm64) SeqGate_1.14.0.tgz
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