- recipe bioconductor-splicewiz
interactive analysis and visualization of alternative splicing in R
- Homepage:
https://bioconductor.org/packages/3.20/bioc/html/SpliceWiz.html
- License:
MIT + file LICENSE
- Recipe:
The analysis and visualization of alternative splicing (AS) events from RNA sequencing data remains challenging. SpliceWiz is a user-friendly and performance-optimized R package for AS analysis, by processing alignment BAM files to quantify read counts across splice junctions, IRFinder-based intron retention quantitation, and supports novel splicing event identification. We introduce a novel visualization for AS using normalized coverage, thereby allowing visualization of differential AS across conditions. SpliceWiz features a shiny-based GUI facilitating interactive data exploration of results including gene ontology enrichment. It is performance optimized with multi-threaded processing of BAM files and a new COV file format for fast recall of sequencing coverage. Overall, SpliceWiz streamlines AS analysis, enabling reliable identification of functionally relevant AS events for further characterization.
- package bioconductor-splicewiz¶
- versions:
1.8.0-0,1.4.0-0,1.2.2-0,1.0.0-1,1.0.0-0- depends bioconductor-annotationhub:
>=3.14.0,<3.15.0- depends bioconductor-annotationhub:
>=3.14.0,<3.15.0a0- depends bioconductor-biocfilecache:
>=2.14.0,<2.15.0- depends bioconductor-biocfilecache:
>=2.14.0,<2.15.0a0- depends bioconductor-biocgenerics:
>=0.52.0,<0.53.0- depends bioconductor-biocgenerics:
>=0.52.0,<0.53.0a0- depends bioconductor-biocparallel:
>=1.40.0,<1.41.0- depends bioconductor-biocparallel:
>=1.40.0,<1.41.0a0- depends bioconductor-biostrings:
>=2.74.0,<2.75.0- depends bioconductor-biostrings:
>=2.74.0,<2.75.0a0- depends bioconductor-bsgenome:
>=1.74.0,<1.75.0- depends bioconductor-bsgenome:
>=1.74.0,<1.75.0a0- depends bioconductor-delayedarray:
>=0.32.0,<0.33.0- depends bioconductor-delayedarray:
>=0.32.0,<0.33.0a0- depends bioconductor-delayedmatrixstats:
>=1.28.0,<1.29.0- depends bioconductor-delayedmatrixstats:
>=1.28.0,<1.29.0a0- depends bioconductor-genefilter:
>=1.88.0,<1.89.0- depends bioconductor-genefilter:
>=1.88.0,<1.89.0a0- depends bioconductor-genomeinfodb:
>=1.42.0,<1.43.0- depends bioconductor-genomeinfodb:
>=1.42.0,<1.43.0a0- depends bioconductor-genomicranges:
>=1.58.0,<1.59.0- depends bioconductor-genomicranges:
>=1.58.0,<1.59.0a0- depends bioconductor-hdf5array:
>=1.34.0,<1.35.0- depends bioconductor-hdf5array:
>=1.34.0,<1.35.0a0- depends bioconductor-iranges:
>=2.40.0,<2.41.0- depends bioconductor-iranges:
>=2.40.0,<2.41.0a0- depends bioconductor-nxtirfdata:
>=1.12.0,<1.13.0- depends bioconductor-nxtirfdata:
>=1.12.0,<1.13.0a0- depends bioconductor-ompbam:
>=1.10.0,<1.11.0- depends bioconductor-ompbam:
>=1.10.0,<1.11.0a0- depends bioconductor-rhdf5:
>=2.50.0,<2.51.0- depends bioconductor-rhdf5:
>=2.50.0,<2.51.0a0- depends bioconductor-rtracklayer:
>=1.66.0,<1.67.0- depends bioconductor-rtracklayer:
>=1.66.0,<1.67.0a0- depends bioconductor-s4vectors:
>=0.44.0,<0.45.0- depends bioconductor-s4vectors:
>=0.44.0,<0.45.0a0- depends bioconductor-summarizedexperiment:
>=1.36.0,<1.37.0- depends bioconductor-summarizedexperiment:
>=1.36.0,<1.37.0a0- depends libblas:
>=3.9.0,<4.0a0- depends libgcc:
>=13- depends liblapack:
>=3.9.0,<4.0a0- depends liblzma:
>=5.6.3,<6.0a0- depends libstdcxx:
>=13- depends libzlib:
>=1.3.1,<2.0a0- depends r-base:
>=4.4,<4.5.0a0- depends r-data.table:
- depends r-dt:
- depends r-fst:
- depends r-ggplot2:
- depends r-heatmaply:
- depends r-htmltools:
- depends r-httr:
- depends r-magrittr:
- depends r-matrixstats:
- depends r-patchwork:
- depends r-pheatmap:
- depends r-plotly:
- depends r-progress:
- depends r-r.utils:
- depends r-rcolorbrewer:
- depends r-rcpp:
>=1.0.5- depends r-rcppprogress:
- depends r-rhandsontable:
- depends r-rsqlite:
- depends r-rvest:
- depends r-scales:
- depends r-shiny:
- depends r-shinydashboard:
- depends r-shinyfiles:
- depends r-shinywidgets:
- depends r-stringi:
- requirements:
- additional platforms:
Installation
You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install bioconductor-splicewiz and update with:: mamba update bioconductor-splicewiz
To create a new environment, run:
mamba create --name myenvname bioconductor-splicewiz
with
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).Alternatively, 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)
