- 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:
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¶
-
- Versions:
1.0.0-0
- Depends:
bioconductor-annotationhub
>=3.6.0,<3.7.0
bioconductor-biocfilecache
>=2.6.0,<2.7.0
bioconductor-biocgenerics
>=0.44.0,<0.45.0
bioconductor-biocparallel
>=1.32.0,<1.33.0
bioconductor-biostrings
>=2.66.0,<2.67.0
bioconductor-bsgenome
>=1.66.0,<1.67.0
bioconductor-delayedarray
>=0.24.0,<0.25.0
bioconductor-delayedmatrixstats
>=1.20.0,<1.21.0
bioconductor-genefilter
>=1.80.0,<1.81.0
bioconductor-genomeinfodb
>=1.34.0,<1.35.0
bioconductor-genomicranges
>=1.50.0,<1.51.0
bioconductor-hdf5array
>=1.26.0,<1.27.0
bioconductor-iranges
>=2.32.0,<2.33.0
bioconductor-nxtirfdata
>=1.4.0,<1.5.0
bioconductor-ompbam
>=1.2.0,<1.3.0
bioconductor-rhdf5
>=2.42.0,<2.43.0
bioconductor-rtracklayer
>=1.58.0,<1.59.0
bioconductor-s4vectors
>=0.36.0,<0.37.0
bioconductor-summarizedexperiment
>=1.28.0,<1.29.0
bioconductor-zlibbioc
>=1.44.0,<1.45.0
libblas
>=3.9.0,<4.0a0
libgcc-ng
>=12
liblapack
>=3.9.0,<4.0a0
libstdcxx-ng
>=12
r-base
>=4.2,<4.3.0a0
r-rcpp
>=1.0.5
- 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>
)
Download stats¶
Link to this page¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-splicewiz/README.html)