ExCluster

DOI: 10.18129/B9.bioc.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: Release (3.8)

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>

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

Installation

To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("ExCluster", version = "3.8")

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, RNASeq, Software
Version 1.0.0
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_1.0.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) ExCluster_1.0.0.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 http://bioconductor.org/packages/ExCluster/
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