Package: ExCluster
Title: ExCluster robustly detects differentially expressed exons
        between two conditions of RNA-seq data, requiring at least two
        independent biological replicates per condition
Version: 1.31.1
Author: R. Matthew Tanner, William L. Stanford, and Theodore J. Perkins
Date: 2018-10-02
Maintainer: R. Matthew Tanner <rtann038@uottawa.ca>
Description: 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.
biocViews: ImmunoOncology, DifferentialSplicing, RNASeq, Software
Imports: stats, methods, grDevices, graphics, utils
Depends: Rsubread, GenomicRanges, rtracklayer, matrixStats, IRanges
License: GPL-3
Encoding: UTF-8
Config/Bioconductor/UnsupportedPlatforms: windows
Config/pak/sysreqs: make libbz2-dev liblzma-dev libxml2-dev libssl-dev
        xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-05-29 18:37:12 UTC
RemoteUrl: https://github.com/bioc/ExCluster
RemoteRef: HEAD
RemoteSha: d9404b890d5654e111aa70c90a731f23535eae72
NeedsCompilation: no
Packaged: 2026-07-12 05:14:34 UTC; root