Package: SeqGate 1.17.0

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]

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SeqGate.pdf |SeqGate.html✨
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-1.17.0(bioc 3.21)SeqGate-1.16.0(bioc 3.20)

differentialexpressiongeneexpressiontranscriptomicssequencingrnaseq

3.30 score 3 scripts 225 downloads 1 exports 29 dependencies

Last updated 5 months agofrom:9990f13d6c. Checks:9 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 30 2025
R-4.5-winOKMar 30 2025
R-4.5-macOKMar 30 2025
R-4.5-linuxOKMar 30 2025
R-4.4-winOKMar 30 2025
R-4.4-macOKMar 30 2025
R-4.4-linuxOKMar 30 2025
R-4.3-winOKMar 30 2025
R-4.3-macOKMar 30 2025

Exports:applySeqGate

Dependencies:abindaskpassBiobaseBiocGenericsBiocManagercrayoncurlDelayedArraygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitelatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6S4ArraysS4VectorsSparseArraySummarizedExperimentsysUCSC.utilsXVector

SeqGate: Filter lowly expressed features

Christelle Reynès, Stéphanie Rialle

Rendered fromSeqgate-html-vignette.Rmdusingknitr::rmarkdownon Mar 30 2025.

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