Package Recipe 'bioconductor-eventpointer'

recipe bioconductor-eventpointer

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

Homepage:: https://bioconductor.org/packages/3.20/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:

3.18.0-0, 3.14.0-0, 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,

3.18.0-0, 3.14.0-0, 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:

on bioconductor-affxparser >=1.82.0,<1.83.0
on bioconductor-affxparser >=1.82.0,<1.83.0a0
on bioconductor-biostrings >=2.78.0,<2.79.0
on bioconductor-biostrings >=2.78.0,<2.79.0a0
on bioconductor-bsgenome >=1.78.0,<1.79.0
on bioconductor-bsgenome >=1.78.0,<1.79.0a0
on bioconductor-fgsea >=1.36.0,<1.37.0
on bioconductor-fgsea >=1.36.2,<1.37.0a0
on bioconductor-genomeinfodb >=1.46.0,<1.47.0
on bioconductor-genomeinfodb >=1.46.2,<1.47.0a0
on bioconductor-genomicfeatures >=1.62.0,<1.63.0
on bioconductor-genomicfeatures >=1.62.0,<1.63.0a0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-genomicranges >=1.62.1,<1.63.0a0
on bioconductor-graph >=1.88.0,<1.89.0
on bioconductor-graph >=1.88.1,<1.89.0a0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-iranges >=2.44.0,<2.45.0a0
on bioconductor-limma >=3.66.0,<3.67.0
on bioconductor-limma >=3.66.0,<3.67.0a0
on bioconductor-qvalue >=2.42.0,<2.43.0
on bioconductor-qvalue >=2.42.0,<2.43.0a0
on bioconductor-rbgl >=1.86.0,<1.87.0
on bioconductor-rbgl >=1.86.0,<1.87.0a0
on bioconductor-rhdf5 >=2.54.0,<2.55.0
on bioconductor-rhdf5 >=2.54.1,<2.55.0a0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-s4vectors >=0.48.0,<0.49.0a0
on bioconductor-sgseq >=1.44.0,<1.45.0
on bioconductor-sgseq >=1.44.0,<1.45.0a0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0a0
on bioconductor-tximport >=1.38.0,<1.39.0
on bioconductor-tximport >=1.38.2,<1.39.0a0
on libblas >=3.9.0,<4.0a0
on libgcc >=14
on liblapack >=3.9.0,<4.0a0
on liblzma >=5.8.2,<6.0a0
on libzlib >=1.3.1,<2.0a0
on r-abind
on r-base >=4.5,<4.6.0a0
on r-cobs
on r-doparallel
on r-foreach
on r-glmnet
on r-igraph
on r-iterators
on r-lpsolve
on r-mass
on r-matrix
on r-matrixstats
on r-nnls
on r-poibin
on r-prodlim
on r-speedglm
on r-stringr

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-eventpointer

to add into an existing workspace instead, run:

pixi add bioconductor-eventpointer

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-eventpointer

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-eventpointer

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

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)