HTSFilter

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see HTSFilter.

Filter replicated high-throughput transcriptome sequencing data


Bioconductor version: 3.9

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 inra.fr>

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

Installation

To install this package, start R (version "3.6") 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 Vignette PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews DifferentialExpression, GeneExpression, ImmunoOncology, Normalization, Preprocessing, RNASeq, Sequencing, Software
Version 1.24.0
In Bioconductor since BioC 2.12 (R-3.0) (11 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
System Requirements
URL
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Suggests EDASeq(>= 2.1.4), BiocStyle, testthat
Linking To
Enhances
Depends On Me
Imports Me coseq
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package HTSFilter_1.24.0.tar.gz
Windows Binary HTSFilter_1.24.0.zip
Mac OS X 10.11 (El Capitan) HTSFilter_1.24.0.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
Old Source Packages for BioC 3.9 Source Archive