recipe bioconductor-splicewiz

Easy, optimized, and accurate alternative splicing analysis in R

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/SpliceWiz.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-splicewiz/meta.yaml

Reads and fragments aligned to splice junctions can be used to quantify alternative splicing events (ASE). However, overlapping ASEs can confound their quantification. SpliceWiz quantifies ASEs, calculating percent-spliced-in (PSI) using junction reads, and intron retention using IRFinder-based quantitation. Novel filters identify ASEs that are relatively less confounded by overlapping events, whereby PSIs can be calculated with higher confidence. SpliceWiz is ultra-fast, using multi-threaded processing of BAM files. It can be run using a graphical user or command line interfaces. GUI-based interactive visualization of differential ASEs, including novel group-based RNA-seq coverage visualization, simplifies short-read RNA-seq analysis in R.

package bioconductor-splicewiz

(downloads) docker_bioconductor-splicewiz

Versions:

1.0.0-0

Depends:
Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-splicewiz

and update with:

conda update bioconductor-splicewiz

or use the docker container:

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

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

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