Introduction: SeqGate method description | Installation | Filtering with SeqGate | Input data | Toy dataset | Getting the SummarizedExperiment input | Filtering with default options | Setting custom filtering parameters | Parameters detailed explanation | Custom filtering parameters example | SessionInfo
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:
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✨
DESCRIPTION |NEWS
card.svg |card.png
SeqGate/json (API)
| # 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:
- data_MiTF_1000genes - Extract of a Transciptome Dataset from Human Melanoma Cell Line
On BioConductor:SeqGate-1.23.0(bioc 3.24)SeqGate-1.22.0(bioc 3.23)
differentialexpressiongeneexpressiontranscriptomicssequencingrnaseq
Last updated from:4449ab3582. Checks:1 ERROR, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 162 | ||
| linux-devel-x86_64 | OK | 246 | ||
| source / vignettes | OK | 219 | ||
| linux-release-x86_64 | OK | 243 | ||
| macos-release-arm64 | OK | 131 | ||
| macos-oldrel-arm64 | OK | 182 | ||
| windows-devel | OK | 193 | ||
| windows-release | OK | 179 | ||
| windows-oldrel | OK | 176 | ||
| wasm-release | OK | 111 |
Exports:applySeqGate
Dependencies:abindBiobaseBiocGenericsBiocManagerDelayedArraygenericsGenomicRangesIRangeslatticeMatrixMatrixGenericsmatrixStatsS4ArraysS4VectorsSeqinfoSparseArraySummarizedExperimentXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Filtering of Lowly Expressed Features | SeqGate-package SeqGate |
| Performs a Filtering of Lowly Expressed Features | applySeqGate seqGate seqgate |
| Extract of a Transciptome Dataset from Human Melanoma Cell Line | data_MITF_1000genes data_MiTF_1000genes data_mitf_1000genes |
