recipe bioconductor-eventpointer

An effective identification of alternative splicing events using junction arrays and RNA-Seq data

Homepage

https://bioconductor.org/packages/3.10/bioc/html/EventPointer.html

License

Artistic-2.0

Recipe

/bioconductor-eventpointer/meta.yaml

EventPointer is an R package to identify alternative splicing events that involve either simple (case-control experiment) or complex experimental designs such as time course experiments and studies including paired-samples. The algorithm can be used to analyze data from either junction arrays (Affymetrix Arrays) or sequencing data (RNA-Seq). The software returns a data.frame with the detected alternative splicing events: gene name, type of event (cassette, alternative 3’,…,etc), genomic position, statistical significance and increment of the percent spliced in (Delta PSI) for all the events. The algorithm can generate a series of files to visualize the detected alternative splicing events in IGV. This eases the interpretation of results and the design of primers for standard PCR validation.

package bioconductor-eventpointer

Versions

2.4.0-0, 2.2.4-0, 2.0.1-0

Depends

• bioconductor-affxparser >=1.58.0,<1.59.0

• bioconductor-biostrings >=2.54.0,<2.55.0

• bioconductor-bsgenome >=1.54.0,<1.55.0

• bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0

• bioconductor-genomeinfodb >=1.22.0,<1.23.0

• bioconductor-genomicfeatures >=1.38.0,<1.39.0

• bioconductor-genomicranges >=1.38.0,<1.39.0

• bioconductor-graph >=1.64.0,<1.65.0

• bioconductor-iranges >=2.20.0,<2.21.0

• bioconductor-limma >=3.42.0,<3.43.0

• bioconductor-qvalue >=2.18.0,<2.19.0

• bioconductor-rbgl >=1.62.0,<1.63.0

• bioconductor-rhdf5 >=2.30.0,<2.31.0

• bioconductor-s4vectors >=0.24.0,<0.25.0

• bioconductor-sgseq >=1.20.0,<1.21.0

• bioconductor-summarizedexperiment >=1.16.0,<1.17.0

• r-base >=3.6,<3.7.0a0

• r-cobs

• r-doparallel

• r-foreach

• r-igraph

• r-mass

• r-matrix

• r-matrixstats

• r-nnls

• r-prodlim

• r-stringr

Required By

Installation

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

conda install bioconductor-eventpointer

and update with:

conda update bioconductor-eventpointer

or use the docker container:

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

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

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-eventpointer/README.html)