FRASER

DOI: 10.18129/B9.bioc.FRASER    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see FRASER.

Find RAre Splicing Events in RNA-Seq Data

Bioconductor version: 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>

Installation

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

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

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	1.2.1
In Bioconductor since	BioC 3.11 (R-4.0) (1 year)
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_1.2.1.tar.gz
Windows Binary	FRASER_1.2.1.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	FRASER_1.2.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/FRASER
Source Repository (Developer Access)	git clone [email protected]:packages/FRASER
Package Short Url	https://bioconductor.org/packages/FRASER/
Package Downloads Report	Download Stats