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

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-data.table

• r-dt

• r-fst

• r-ggplot2

• r-heatmaply

• r-magrittr

• r-matrixstats

• r-pheatmap

• r-plotly

• r-progress

• r-r.utils

• r-rcolorbrewer

• r-rcpp >=1.0.5

• r-rcppprogress

• r-rhandsontable

• r-shiny

• r-shinydashboard

• r-shinyfiles

• r-shinywidgets

• r-xml

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:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-splicewiz/README.html)