FRASER
This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see FRASER.
Find RAre Splicing Events in RNA-Seq Data
Bioconductor version: 3.17
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("FRASER")):
Installation
To install this package, start R (version "4.3") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | AlternativeSplicing, Coverage, Genetics, RNASeq, Sequencing, Software |
| Version | 1.12.1 |
| 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 |
See More
| 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_1.12.1.tar.gz |
| Windows Binary | FRASER_1.12.1.zip |
| macOS Binary (x86_64) | FRASER_1.12.1.tgz |
| macOS Binary (arm64) | FRASER_1.12.1.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 3.17 | Source Archive |