recipe bioconductor-excluster

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

Homepage

https://bioconductor.org/packages/3.12/bioc/html/ExCluster.html

License

GPL-3

Recipe

/bioconductor-excluster/meta.yaml

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.

package bioconductor-excluster

Versions

1.8.0-0,  1.6.0-0,  1.4.0-0,  1.2.0-1,  1.0.0-0

Depends

• bioconductor-genomicranges >=1.42.0,<1.43.0

• bioconductor-iranges >=2.24.0,<2.25.0

• bioconductor-rsubread >=2.4.0,<2.5.0

• bioconductor-rtracklayer >=1.50.0,<1.51.0

• r-base >=4.0,<4.1.0a0

• r-matrixstats

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-excluster

and update with:

conda update bioconductor-excluster

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-excluster:<tag>

(see bioconductor-excluster/tags for valid values for <tag>)

Link to this page

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