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HTSFilter

Filter replicated high-throughput transcriptome sequencing data


Bioconductor version: Release (3.19)

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 Jaffr├ęzic [ctb]

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

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

Installation

To install this package, start R (version "4.4") 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")
HTSFilter HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DifferentialExpression, GeneExpression, ImmunoOncology, Normalization, Preprocessing, RNASeq, Sequencing, Software
Version 1.44.0
In Bioconductor since BioC 2.12 (R-3.0) (11 years)
License Artistic-2.0
Depends R (>= 4.0.0)
Imports edgeR, DESeq2, BiocParallel, Biobase, utils, stats, grDevices, graphics, methods
System Requirements
URL
See More
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_1.44.0.tar.gz
Windows Binary HTSFilter_1.44.0.zip (64-bit only)
macOS Binary (x86_64) HTSFilter_1.44.0.tgz
macOS Binary (arm64) HTSFilter_1.44.0.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