- recipe bioconductor-eventpointer
An effective identification of alternative splicing events using junction arrays and RNA-Seq data
- Homepage:
https://bioconductor.org/packages/3.16/bioc/html/EventPointer.html
- License:
Artistic-2.0
- Recipe:
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:
3.6.0-1
,3.6.0-0
,3.2.0-2
,3.2.0-1
,3.2.0-0
,3.0.0-0
,2.8.0-1
,2.8.0-0
,2.6.0-0
,3.6.0-1
,3.6.0-0
,3.2.0-2
,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
>=1.70.0,<1.71.0
bioconductor-biostrings
>=2.66.0,<2.67.0
bioconductor-bsgenome
>=1.66.0,<1.67.0
bioconductor-fgsea
>=1.24.0,<1.25.0
bioconductor-genomeinfodb
>=1.34.0,<1.35.0
bioconductor-genomicfeatures
>=1.50.0,<1.51.0
bioconductor-genomicranges
>=1.50.0,<1.51.0
bioconductor-graph
>=1.76.0,<1.77.0
bioconductor-iranges
>=2.32.0,<2.33.0
bioconductor-limma
>=3.54.0,<3.55.0
bioconductor-qvalue
>=2.30.0,<2.31.0
bioconductor-rbgl
>=1.74.0,<1.75.0
bioconductor-rhdf5
>=2.42.0,<2.43.0
bioconductor-s4vectors
>=0.36.0,<0.37.0
bioconductor-sgseq
>=1.32.0,<1.33.0
bioconductor-summarizedexperiment
>=1.28.0,<1.29.0
bioconductor-tximport
>=1.26.0,<1.27.0
libblas
>=3.9.0,<4.0a0
libgcc-ng
>=12
liblapack
>=3.9.0,<4.0a0
r-base
>=4.2,<4.3.0a0
- 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¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-eventpointer/README.html)