Package: HTSFilter 1.52.0

Andrea Rau

HTSFilter: Filter replicated high-throughput transcriptome sequencing data

This package implements a filtering procedure for replicated transcriptome sequencing data based on a global Jaccard similarity index in order to identify genes with low, constant levels of expression across one or more experimental conditions.

Authors:Andrea Rau [cre, aut], Melina Gallopin [ctb], Gilles Celeux [ctb], Florence Jaffrézic [ctb]

HTSFilter_1.52.0.tar.gz
HTSFilter_1.52.0.zip(r-4.7)HTSFilter_1.52.0.zip(r-4.6)HTSFilter_1.52.0.zip(r-4.5)
HTSFilter_1.52.0.tgz(r-4.6-any)HTSFilter_1.52.0.tgz(r-4.5-any)
HTSFilter_1.52.0.tar.gz(r-4.7-any)HTSFilter_1.52.0.tar.gz(r-4.6-any)
HTSFilter_1.52.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
HTSFilter/json (API)
NEWS

# Install 'HTSFilter' in R:

install.packages('HTSFilter', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

sultan - RNA-seq data from humans in Sultan et al.

On BioConductor:HTSFilter-1.53.0(bioc 3.24)HTSFilter-1.52.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

sequencing rnaseq preprocessing differentialexpression geneexpression normalization immunooncology

6.43 score 2 packages 45 scripts 552 downloads 35 mentions 3 exports 49 dependencies

Last updated from:40d8543075 (on RELEASE_3_23). Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: no.

Target	Result	Time
bioc-checks	WARNING	175
linux-devel-x86_64	NOTE	348
source / vignettes	OK	323
linux-release-x86_64	NOTE	340
macos-release-arm64	NOTE	173
macos-oldrel-arm64	NOTE	154
windows-devel	NOTE	229
windows-release	NOTE	215
windows-oldrel	NOTE	219
wasm-release	OK	164

Exports:HTSBasicFilter HTSFilter normalizeData

Dependencies:abind BH Biobase BiocGenerics BiocParallel cli codetools cpp11 DelayedArray DESeq2 edgeR farver formatR futile.logger futile.options generics GenomicRanges ggplot2 glue gtable IRanges isoband labeling lambda.r lattice lifecycle limma locfit Matrix MatrixGenerics matrixStats R6 RColorBrewer Rcpp RcppArmadillo rlang S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray statmod SummarizedExperiment vctrs viridisLite withr XVector

HTSFilter package: Quick-start guide

Andrea Rau, Mélina Gallopin, Gilles Celeux, Florence Jaffrézic

Rendered fromHTSFilter.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2020-11-26
Started: 2020-11-26

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Filter replicated high-throughput transcriptome sequencing data	HTSFilter-package
Implement basic filters for transcriptome sequencing data.	HTSBasicFilter HTSBasicFilter,data.frame-method HTSBasicFilter,DESeqDataSet-method HTSBasicFilter,DGEExact-method HTSBasicFilter,DGEGLM-method HTSBasicFilter,DGEList-method HTSBasicFilter,DGELRT-method HTSBasicFilter,matrix-method
Calculate data-based filtering threshold for replicated transcriptome sequencing data.	HTSFilter HTSFilter,data.frame-method HTSFilter,DESeqDataSet-method HTSFilter,DGEExact-method HTSFilter,DGEGLM-method HTSFilter,DGEList-method HTSFilter,DGELRT-method HTSFilter,matrix-method HTSFilter-methods
Normalize transcriptome sequencing data.	normalizeData
RNA-seq data from humans in Sultan et al. (2008)	sultan