Package: SeqGate 1.23.0

Stéphanie Rialle

SeqGate: Filtering of Lowly Expressed Features

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.

Authors:Christelle Reynès [aut], Stéphanie Rialle [aut, cre]

SeqGate_1.23.0.tar.gz
SeqGate_1.23.0.zip(r-4.7)SeqGate_1.23.0.zip(r-4.6)SeqGate_1.23.0.zip(r-4.5)
SeqGate_1.23.0.tgz(r-4.6-any)SeqGate_1.23.0.tgz(r-4.5-any)
SeqGate_1.23.0.tar.gz(r-4.7-any)SeqGate_1.23.0.tar.gz(r-4.6-any)
SeqGate_1.23.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
SeqGate/json (API)
NEWS

# Install 'SeqGate' in R:
install.packages('SeqGate', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/srialle/seqgate/issues

Datasets:

On BioConductor:SeqGate-1.23.0(bioc 3.24)SeqGate-1.22.0(bioc 3.23)

differentialexpressiongeneexpressiontranscriptomicssequencingrnaseq

3.30 score 7 scripts 318 downloads 1 exports 18 dependencies

Last updated from:4449ab3582. Checks:1 ERROR, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR162
linux-devel-x86_64OK246
source / vignettesOK219
linux-release-x86_64OK243
macos-release-arm64OK131
macos-oldrel-arm64OK182
windows-develOK193
windows-releaseOK179
windows-oldrelOK176
wasm-releaseOK111

Exports:applySeqGate

Dependencies:abindBiobaseBiocGenericsBiocManagerDelayedArraygenericsGenomicRangesIRangeslatticeMatrixMatrixGenericsmatrixStatsS4ArraysS4VectorsSeqinfoSparseArraySummarizedExperimentXVector

SeqGate: Filter lowly expressed features

Christelle Reynès, Stéphanie Rialle

Rendered fromSeqgate-html-vignette.Rmdusingknitr::rmarkdownon May 31 2026.

Last update: 2021-01-19
Started: 2020-07-10

Readme and manuals

Help Manual

Help pageTopics
Filtering of Lowly Expressed FeaturesSeqGate-package SeqGate
Performs a Filtering of Lowly Expressed FeaturesapplySeqGate seqGate seqgate
Extract of a Transciptome Dataset from Human Melanoma Cell Linedata_MITF_1000genes data_MiTF_1000genes data_mitf_1000genes