HTSFilter

This is the development version of HTSFilter; for the stable release version, see HTSFilter.

Filter replicated high-throughput transcriptome sequencing data

Bioconductor version: Development (3.21)

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] (ORCID: ), Melina Gallopin [ctb], Gilles Celeux [ctb], Florence Jaffrézic [ctb]

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

Citation (from within R, enter citation("HTSFilter")):

Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

HTSFilter	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DifferentialExpression, GeneExpression, ImmunoOncology, Normalization, Preprocessing, RNASeq, Sequencing, Software
Version	1.47.0
In Bioconductor since	BioC 2.12 (R-3.0) (11.5 years)
License	Artistic-2.0
Depends	R (>= 4.0.0)
Imports	edgeR, DESeq2, BiocParallel, Biobase, utils, stats, grDevices, graphics, methods
System Requirements
URL

Suggests	EDASeq, testthat, knitr, rmarkdown, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me	coseq
Suggests Me	HTSCluster
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	HTSFilter_1.47.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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