FRASER
This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see FRASER.
Find RAre Splicing Events in RNA-Seq Data
Bioconductor version: 3.12
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("FRASER")):
Installation
To install this package, start R (version "4.0") 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 | 1.2.1 |
| 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_1.2.1.tar.gz |
| Windows Binary | FRASER_1.2.1.zip (32- & 64-bit) |
| macOS 10.13 (High Sierra) | FRASER_1.2.1.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 3.12 | Source Archive |