- recipe bioconductor-eventpointer
An effective identification of alternative splicing events using junction arrays and RNA-Seq data
- Homepage:
https://bioconductor.org/packages/3.18/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:
3.10.0-0,3.8.0-0,3.6.0-1,3.6.0-0,3.2.0-2,3.2.0-1,3.2.0-0,3.0.0-0,2.8.0-1,3.10.0-0,3.8.0-0,3.6.0-1,3.6.0-0,3.2.0-2,3.2.0-1,3.2.0-0,3.0.0-0,2.8.0-1,2.8.0-0,2.6.0-0,2.4.0-0,2.2.4-0,2.0.1-0- depends bioconductor-affxparser:
>=1.74.0,<1.75.0- depends bioconductor-affxparser:
>=1.74.0,<1.75.0a0- depends bioconductor-biostrings:
>=2.70.0,<2.71.0- depends bioconductor-biostrings:
>=2.70.1,<2.71.0a0- depends bioconductor-bsgenome:
>=1.70.0,<1.71.0- depends bioconductor-bsgenome:
>=1.70.1,<1.71.0a0- depends bioconductor-fgsea:
>=1.28.0,<1.29.0- depends bioconductor-fgsea:
>=1.28.0,<1.29.0a0- depends bioconductor-genomeinfodb:
>=1.38.0,<1.39.0- depends bioconductor-genomeinfodb:
>=1.38.1,<1.39.0a0- depends bioconductor-genomicfeatures:
>=1.54.0,<1.55.0- depends bioconductor-genomicfeatures:
>=1.54.1,<1.55.0a0- depends bioconductor-genomicranges:
>=1.54.0,<1.55.0- depends bioconductor-genomicranges:
>=1.54.1,<1.55.0a0- depends bioconductor-graph:
>=1.80.0,<1.81.0- depends bioconductor-graph:
>=1.80.0,<1.81.0a0- depends bioconductor-iranges:
>=2.36.0,<2.37.0- depends bioconductor-iranges:
>=2.36.0,<2.37.0a0- depends bioconductor-limma:
>=3.58.0,<3.59.0- depends bioconductor-limma:
>=3.58.1,<3.59.0a0- depends bioconductor-qvalue:
>=2.34.0,<2.35.0- depends bioconductor-qvalue:
>=2.34.0,<2.35.0a0- depends bioconductor-rbgl:
>=1.78.0,<1.79.0- depends bioconductor-rbgl:
>=1.78.0,<1.79.0a0- depends bioconductor-rhdf5:
>=2.46.0,<2.47.0- depends bioconductor-rhdf5:
>=2.46.1,<2.47.0a0- depends bioconductor-s4vectors:
>=0.40.0,<0.41.0- depends bioconductor-s4vectors:
>=0.40.2,<0.41.0a0- depends bioconductor-sgseq:
>=1.36.0,<1.37.0- depends bioconductor-sgseq:
>=1.36.0,<1.37.0a0- depends bioconductor-summarizedexperiment:
>=1.32.0,<1.33.0- depends bioconductor-summarizedexperiment:
>=1.32.0,<1.33.0a0- depends bioconductor-tximport:
>=1.30.0,<1.31.0- depends bioconductor-tximport:
>=1.30.0,<1.31.0a0- depends libblas:
>=3.9.0,<4.0a0- depends libgcc-ng:
>=12- depends liblapack:
>=3.9.0,<4.0a0- depends r-abind:
- depends r-base:
>=4.3,<4.4.0a0- depends r-cobs:
- depends r-doparallel:
- depends r-foreach:
- depends r-glmnet:
- depends r-igraph:
- depends r-iterators:
- depends r-lpsolve:
- depends r-mass:
- depends r-matrix:
- depends r-matrixstats:
- depends r-nnls:
- depends r-poibin:
- depends r-prodlim:
- depends r-speedglm:
- depends r-stringr:
- requirements:
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-eventpointer and update with:: mamba update bioconductor-eventpointer
To create a new environment, run:
mamba create --name myenvname bioconductor-eventpointer
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-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)
