Bioconductor - EventPointer

Bioconductor - EventPointer
Bioconductor 3.22
Software Packages
EventPointer
EventPointer
This is the
released
version of EventPointer; for the devel version, see
EventPointer
An effective identification of alternative splicing events using junction arrays and RNA-Seq data
DOI:
10.18129/B9.bioc.EventPointer
Bioconductor version:
Release (3.22)
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.
Author:
Juan Pablo Romero [aut], Juan A. Ferrer-Bonsoms [aut, cre], Pablo Sacristan [aut], Ander Muniategui [aut], Fernando Carazo [aut], Ander Aramburu [aut], Angel Rubio [aut]
Maintainer:
Juan A. Ferrer-Bonsoms
Citation (from within R, enter
citation("EventPointer")
):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")

BiocManager::install("EventPointer")
For older versions of R, please refer to the appropriate
Bioconductor release
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("EventPointer")
EventPointer
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Reference Manual
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NEWS
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Details
biocViews
AlternativeSplicing
DifferentialSplicing
ImmunoOncology
RNASeq
Sequencing
Software
TimeCourse
Transcription
mRNAMicroarray
Version
3.18.0
In Bioconductor since
BioC 3.5 (R-3.4) (9 years)
License
Artistic-2.0
Depends
R (>= 3.5.0),
SGSeq
Matrix
SummarizedExperiment
Imports
GenomicFeatures
stringr
GenomeInfoDb
igraph
MASS
nnls
limma
matrixStats
RBGL
prodlim
graph
, methods, utils, stats,
doParallel
foreach
affxparser
GenomicRanges
S4Vectors
IRanges
qvalue
cobs
rhdf5
BSgenome
Biostrings
glmnet
abind
iterators
lpSolve
poibin
speedglm
tximport
fgsea
System Requirements
URL
Bug Reports
See More
Suggests
knitr
rmarkdown
BiocStyle
RUnit
BiocGenerics
dplyr
kableExtra
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
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Installation
instructions to use this package in your R session.
Source Package
EventPointer_3.18.0.tar.gz
Windows Binary (x86_64)
EventPointer_3.18.0.zip
macOS Binary (x86_64)
EventPointer_3.18.0.tgz
macOS Binary (arm64)
EventPointer_3.18.0.tgz
Source Repository
git clone https://git.bioconductor.org/packages/EventPointer
Source Repository (Developer Access)
git clone git@git.bioconductor.org:packages/EventPointer
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