Package: HTSFilter 1.53.0

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_1.53.0.tar.gz
HTSFilter_1.53.0.zip(r-4.7)HTSFilter_1.53.0.zip(r-4.6)HTSFilter_1.53.0.zip(r-4.5)
HTSFilter_1.53.0.tgz(r-4.6-any)HTSFilter_1.53.0.tgz(r-4.5-any)
HTSFilter_1.53.0.tar.gz(r-4.7-any)HTSFilter_1.53.0.tar.gz(r-4.6-any)
HTSFilter_1.53.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
HTSFilter/json (API)

# Install 'HTSFilter' in R:

install.packages('HTSFilter', repos = c('https://bioc.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

6.42 score 2 packages 44 scripts 35 mentions 3 exports 49 dependencies

Last updated from:7219a35a2e. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	198
linux-devel-x86_64	NOTE	367
source / vignettes	OK	251
linux-release-x86_64	NOTE	291
macos-release-arm64	NOTE	178
macos-oldrel-arm64	NOTE	163
windows-devel	NOTE	237
windows-release	NOTE	221
windows-oldrel	NOTE	225
wasm-release	OK	196

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

Introduction | Input data | Use of HTSFilter with varying data types | matrix and data.frame classes | edgeR package pipeline | S3 class DGEExact | S3 class DGELRT | DESeq2 package pipeline: S4 class DESeqDataSet} | Alternative normalization using EDAseq | Session Info | References

Rendered fromHTSFilter.Rmdusingknitr::rmarkdown

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