HTSFilter

DOI: 10.18129/B9.bioc.HTSFilter    

Filter replicated high-throughput transcriptome sequencing data

Bioconductor version: Release (3.11)

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, Melina Gallopin, Gilles Celeux, and Florence Jaffrezic

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

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

PDF	R Script	HTSFilter Vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, GeneExpression, ImmunoOncology, Normalization, Preprocessing, RNASeq, Sequencing, Software
Version	1.28.0
In Bioconductor since	BioC 2.12 (R-3.0) (7.5 years)
License	Artistic-2.0
Depends	R (>= 3.4)
Imports	edgeR(>= 3.9.14), DESeq2(>= 1.10.1), DESeq(>= 1.22.1), BiocParallel(>= 1.4.3), Biobase, utils, stats, grDevices, graphics, methods
LinkingTo
Suggests	EDASeq(>= 2.1.4), BiocStyle, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me	coseq
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	HTSFilter_1.28.0.tar.gz
Windows Binary	HTSFilter_1.28.0.zip
macOS 10.13 (High Sierra)	HTSFilter_1.28.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/HTSFilter
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/HTSFilter
Package Short Url	https://bioconductor.org/packages/HTSFilter/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.11	Source Archive