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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 (3.20)

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")

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

Details

biocViews AlternativeSplicing, Coverage, Genetics, RNASeq, Sequencing, Software
Version 2.1.0
In Bioconductor since BioC 3.11 (R-4.0) (4 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
See More
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
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Package Archives

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

Source Package FRASER_2.1.0.tar.gz
Windows Binary FRASER_2.1.0.zip (64-bit only)
macOS Binary (x86_64)
macOS Binary (arm64) FRASER_2.1.0.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