dasper

DOI: 10.18129/B9.bioc.dasper  

This package is for version 3.17 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see dasper.

Detecting abberant splicing events from RNA-sequencing data

Bioconductor version: 3.17

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>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("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	1.9.0
In Bioconductor since	BioC 3.12 (R-4.0) (3 years)
License	Artistic-2.0
Depends	R (>= 4.0)
Imports	basilisk, BiocFileCache, BiocParallel, data.table, dplyr, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, ggpubr, ggrepel, grid, IRanges, magrittr, megadepth, methods, plyranges, readr, reticulate, rtracklayer, S4Vectors, stringr, SummarizedExperiment, tidyr
LinkingTo
Suggests	AnnotationFilter, BiocStyle, covr, ensembldb, GenomicState, knitr, lifecycle, markdown, recount, RefManageR, rmarkdown, sessioninfo, testthat, tibble
SystemRequirements
Enhances
URL	https://github.com/dzhang32/dasper
BugReports	https://support.bioconductor.org/t/dasper
Depends On Me
Imports Me	ODER
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	dasper_1.9.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/dasper
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/dasper
Bioc Package Browser	https://code.bioconductor.org/browse/dasper/
Package Short Url	https://bioconductor.org/packages/dasper/
Package Downloads Report	Download Stats