ExCluster

DOI: 10.18129/B9.bioc.ExCluster    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see ExCluster.

ExCluster robustly detects differentially expressed exons between two conditions of RNA-seq data, requiring at least two independent biological replicates per condition

Bioconductor version: 3.12

ExCluster flattens Ensembl and GENCODE GTF files into GFF files, which are used to count reads per non-overlapping exon bin from BAM files. This read counting is done using the function featureCounts from the package Rsubread. Library sizes are normalized across all biological replicates, and ExCluster then compares two different conditions to detect signifcantly differentially spliced genes. This process requires at least two independent biological repliates per condition, and ExCluster accepts only exactly two conditions at a time. ExCluster ultimately produces false discovery rates (FDRs) per gene, which are used to detect significance. Exon log2 fold change (log2FC) means and variances may be plotted for each significantly differentially spliced gene, which helps scientists develop hypothesis and target differential splicing events for RT-qPCR validation in the wet lab.

Author: R. Matthew Tanner, William L. Stanford, and Theodore J. Perkins

Maintainer: R. Matthew Tanner <rtann038 at uottawa.ca>

Installation

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

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

BiocManager::install("ExCluster")

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("ExCluster")

 

PDF	R Script	ExCluster Vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialSplicing, ImmunoOncology, RNASeq, Software
Version	1.8.0
In Bioconductor since	BioC 3.8 (R-3.5) (2.5 years)
License	GPL-3
Depends	Rsubread, GenomicRanges, rtracklayer, matrixStats, IRanges
Imports	stats, methods, grDevices, graphics, utils
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Package Archives

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

Source Package	ExCluster_1.8.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)	ExCluster_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ExCluster
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ExCluster
Package Short Url	https://bioconductor.org/packages/ExCluster/
Package Downloads Report	Download Stats