recipe bioconductor-eventpointer

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

Homepage:

https://bioconductor.org/packages/3.14/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:

3.2.0-1,  3.2.0-0,  3.0.0-0,  2.8.0-1,  2.8.0-0,  2.6.0-0,  2.4.0-0,  2.2.4-0,  2.0.1-0

Depends:

• bioconductor-affxparser >=1.66.0,<1.67.0

• bioconductor-biostrings >=2.62.0,<2.63.0

• bioconductor-bsgenome >=1.62.0,<1.63.0

• bioconductor-genomeinfodb >=1.30.0,<1.31.0

• bioconductor-genomicfeatures >=1.46.0,<1.47.0

• bioconductor-genomicranges >=1.46.0,<1.47.0

• bioconductor-graph >=1.72.0,<1.73.0

• bioconductor-iranges >=2.28.0,<2.29.0

• bioconductor-limma >=3.50.0,<3.51.0

• bioconductor-qvalue >=2.26.0,<2.27.0

• bioconductor-rbgl >=1.70.0,<1.71.0

• bioconductor-rhdf5 >=2.38.0,<2.39.0

• bioconductor-s4vectors >=0.32.0,<0.33.0

• bioconductor-sgseq >=1.28.0,<1.29.0

• bioconductor-summarizedexperiment >=1.24.0,<1.25.0

• bioconductor-tximport >=1.22.0,<1.23.0

• libblas >=3.8.0,<4.0a0

• libgcc-ng >=10.3.0

• liblapack >=3.8.0,<4.0a0

• r-abind

• r-base >=4.1,<4.2.0a0

• r-cobs

• r-doparallel

• r-foreach

• r-glmnet

• r-igraph

• r-iterators

• r-lpsolve

• r-mass

• r-matrix

• r-matrixstats

• r-nnls

• r-poibin

• r-prodlim

• r-speedglm

• r-stringr

Required By:

Installation

With an activated Bioconda channel (see 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>)

Download stats

Link to this page

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