FRASER

Find RAre Splicing Events in RNA-Seq Data

Bioconductor version: Release (3.20)

Detection of rare aberrant splicing events in transcriptome profiles. Read count ratio expectations are modeled by an autoencoder to control for confounding factors in the data. Given these expectations, the ratios are assumed to follow a beta-binomial distribution with a junction specific dispersion. Outlier events are then identified as read-count ratios that deviate significantly from this distribution. FRASER is able to detect alternative splicing, but also intron retention. The package aims to support 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] , Karoline Lutz [ctb], Vicente Yepez [aut] , 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 "4.4") and enter:


if (!require("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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	AlternativeSplicing, Coverage, Genetics, RNASeq, Sequencing, Software
Version	2.2.0
In Bioconductor since	BioC 3.11 (R-4.0) (4.5 years)
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
System Requirements
URL	https://github.com/gagneurlab/FRASER
Bug Reports	https://github.com/gagneurlab/FRASER/issues

Suggests	magick, BiocStyle, knitr, rmarkdown, testthat, covr, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, rtracklayer, SGSeq, ggbio, biovizBase
Linking To	RcppArmadillo, Rcpp
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	FRASER_2.2.0.tar.gz
Windows Binary (x86_64)	FRASER_2.2.0.zip (64-bit only)
macOS Binary (x86_64)	FRASER_2.2.0.tgz
macOS Binary (arm64)	FRASER_2.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/FRASER
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/FRASER
Bioc Package Browser	https://code.bioconductor.org/browse/FRASER/
Package Short Url	https://bioconductor.org/packages/FRASER/
Package Downloads Report	Download Stats