HTSFilter

DOI: 10.18129/B9.bioc.HTSFilter  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see HTSFilter.

Filter replicated high-throughput transcriptome sequencing data

Bioconductor version: 3.17

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.

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

Maintainer: Andrea Rau <andrea.rau at inrae.fr>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("HTSFilter")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("HTSFilter")

 

HTML	R Script	HTSFilter
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, GeneExpression, ImmunoOncology, Normalization, Preprocessing, RNASeq, Sequencing, Software
Version	1.40.0
In Bioconductor since	BioC 2.12 (R-3.0) (10.5 years)
License	Artistic-2.0
Depends	R (>= 4.0.0)
Imports	edgeR, DESeq2, BiocParallel, Biobase, utils, stats, grDevices, graphics, methods
LinkingTo
Suggests	EDASeq, testthat, knitr, rmarkdown, BiocStyle
SystemRequirements
Enhances
URL
Depends On Me
Imports Me	coseq
Suggests Me	HTSCluster
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	HTSFilter_1.40.0.tar.gz
Windows Binary	HTSFilter_1.40.0.zip
macOS Binary (x86_64)	HTSFilter_1.40.0.tgz
macOS Binary (arm64)	HTSFilter_1.40.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/HTSFilter
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/HTSFilter
Bioc Package Browser	https://code.bioconductor.org/browse/HTSFilter/
Package Short Url	https://bioconductor.org/packages/HTSFilter/
Package Downloads Report	Download Stats