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: 3.23 · Package version: 1.30.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ExCluster")Details
| Maintainer | R. Matthew Tanner <rtann038@uottawa.ca> |
| Author | R. Matthew Tanner, William L. Stanford, and Theodore J. Perkins |
| License | GPL-3 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DifferentialSplicing, ImmunoOncology, RNASeq, Software |
| Package Short Url | https://bioconductor.org/packages/ExCluster/ |
Citation
From within R, enter citation("ExCluster"):
R. Matthew Tanner, William L. Stanford, and Theodore J. Perkins. ExCluster: ExCluster robustly detects differentially expressed exons between two conditions of RNA-seq data, requiring at least two independent biological replicates per condition. doi:10.18129/B9.bioc.ExCluster, R package version 1.30.0, https://bioconductor.org/packages/ExCluster.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | ExCluster_1.30.0.tar.gz |
| Windows binary (x86_64) | ExCluster_1.30.0.zip |
| macOS binary (arm64) | ExCluster_1.30.0.tgz |
| macOS binary (x86_64) | ExCluster_1.30.0.tgz |
Dependencies
Depends: Rsubread, GenomicRanges, rtracklayer, matrixStats, IRanges
Imports: stats, methods, grDevices, graphics, utils