recipe bioconductor-eventpointer

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.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/EventPointer.html

License

Artistic-2.0

Recipe

/bioconductor-eventpointer/meta.yaml

package bioconductor-eventpointer

(downloads) docker_bioconductor-eventpointer

Versions

2.0.1-0

Depends bioconductor-affxparser

>=1.54.0,<1.55.0

Depends bioconductor-genomeinfodb

>=1.18.0,<1.19.0

Depends bioconductor-genomicfeatures

>=1.34.0,<1.35.0

Depends bioconductor-genomicranges

>=1.34.0,<1.35.0

Depends bioconductor-graph

>=1.60.0,<1.61.0

Depends bioconductor-iranges

>=2.16.0,<2.17.0

Depends bioconductor-limma

>=3.38.0,<3.39.0

Depends bioconductor-qvalue

>=2.14.0,<2.15.0

Depends bioconductor-rbgl

>=1.58.0,<1.59.0

Depends bioconductor-rhdf5

>=2.26.0,<2.27.0

Depends bioconductor-s4vectors

>=0.20.0,<0.21.0

Depends bioconductor-sgseq

>=1.16.0,<1.17.0

Depends bioconductor-summarizedexperiment

>=1.12.0,<1.13.0

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-cobs

Depends r-doparallel

Depends r-foreach

Depends r-igraph

Depends r-mass

Depends r-matrix

Depends r-matrixstats

Depends r-nnls

Depends r-prodlim

Depends r-stringr

Requirements

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>)