FRASER

DOI: 10.18129/B9.bioc.FRASER    

This is the development version of FRASER; for the stable release version, see FRASER.

Find RAre Splicing Events in RNA-Seq Data

Bioconductor version: Development (3.12)

Detection of rare aberrant splicing events in transcriptome profiles. The workflow aims to assist the diagnostics in the field of rare diseases where RNA-seq is performed to identify aberrant splicing defects.

Author: Christian Mertes [aut, cre], Ines Scheller [aut], Vicente Yepez [ctb], Julien Gagneur [aut]

Maintainer: Christian Mertes <mertes at in.tum.de>

Citation (from within R, enter citation("FRASER")):

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("FRASER")

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("FRASER")

 

PDF R Script FRASER: Find RAre Splicing Evens in RNA-seq Data
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews AlternativeSplicing, Coverage, Genetics, RNASeq, Sequencing, Software
Version 1.1.6
In Bioconductor since BioC 3.11 (R-4.0) (< 6 months)
License MIT + file LICENSE
Depends BiocParallel, data.table, Rsamtools, SummarizedExperiment
Imports AnnotationDbi, BBmisc, Biobase, BiocGenerics, biomaRt, BSgenome, cowplot, DelayedArray(>= 0.5.11), DelayedMatrixStats, extraDistr, generics, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, IRanges, grDevices, ggplot2, ggrepel, HDF5Array, matrixStats, methods, OUTRIDER, pcaMethods, pheatmap, plotly, PRROC, RColorBrewer, rhdf5, Rsubread, R.utils, S4Vectors, stats, tibble, tools, utils, VGAM
LinkingTo Rcpp, RcppArmadillo
Suggests BiocStyle, knitr, rmarkdown, testthat, covr, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db
SystemRequirements
Enhances
URL https://github.com/gagneurlab/FRASER
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package FRASER_1.1.6.tar.gz
Windows Binary FRASER_1.1.6.zip
macOS 10.13 (High Sierra) FRASER_1.1.6.tgz
Source Repository git clone https://git.bioconductor.org/packages/FRASER
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/FRASER
Package Short Url https://bioconductor.org/packages/FRASER/
Package Downloads Report Download Stats

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