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 (3.16)

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], 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 "4.2") 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")

 

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 1.9.1
In Bioconductor since BioC 3.11 (R-4.0) (2.5 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
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_1.9.1.tar.gz
Windows Binary FRASER_1.9.1.zip
macOS 10.13 (High Sierra) FRASER_1.9.1.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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