FRASER

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see FRASER.

Find RAre Splicing Events in RNA-Seq Data

Bioconductor version: 3.13

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 "4.1") 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 Evens 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 1.4.0

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

Suggests BiocStyle, knitr, rmarkdown, testthat, covr, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db

Linking To Rcpp, RcppArmadillo

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_1.4.0.tar.gz

Windows Binary FRASER_1.4.0.zip (32- & 64-bit)

macOS 10.13 (High Sierra) FRASER_1.4.0.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

Old Source Packages for BioC 3.13 Source Archive