dasper

DOI: 10.18129/B9.bioc.dasper    

Detecting abberant splicing events from RNA-sequencing data

Bioconductor version: Release (3.12)

The aim of dasper is to detect aberrant splicing events from RNA-seq data. dasper will use as input both junction and coverage data from RNA-seq to calculate the deviation of each splicing event in a patient from a set of user-defined controls. dasper uses an unsupervised outlier detection algorithm to score each splicing event in the patient with an outlier score representing the degree to which that splicing event looks abnormal.

Author: David Zhang [aut, cre] , Leonardo Collado-Torres [ctb]

Maintainer: David Zhang <david.zhang.12 at ucl.ac.uk>

Citation (from within R, enter citation("dasper")):

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("dasper")

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("dasper")

 

HTML R Script Introduction to dasper
PDF   Reference Manual
Text   NEWS

Details

biocViews AlternativeSplicing, Coverage, RNASeq, Sequencing, Software, Transcriptomics
Version 1.0.0
In Bioconductor since BioC 3.12 (R-4.0) (< 6 months)
License Artistic-2.0
Depends R (>= 4.0)
Imports basilisk, BiocFileCache, BiocParallel, data.table, dplyr, GenomeInfoDb, GenomicFeatures, GenomicRanges, IRanges, magrittr, megadepth, methods, plyranges, readr, reticulate, S4Vectors, stringr, SummarizedExperiment, tidyr
LinkingTo
Suggests BiocStyle, covr, testthat, GenomicState, ggplot2, ggpubr, ggrepel, grid, knitcitations, knitr, recount, rmarkdown, sessioninfo, rtracklayer, tibble
SystemRequirements
Enhances
URL https://github.com/dzhang32/dasper
BugReports https://support.bioconductor.org/t/dasper
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 dasper_1.0.0.tar.gz
Windows Binary dasper_1.0.0.zip
macOS 10.13 (High Sierra) dasper_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/dasper
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/dasper
Package Short Url https://bioconductor.org/packages/dasper/
Package Downloads Report Download Stats

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