dasper

This package is for version 3.13 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: 3.13

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 "4.1") 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")
Introduction to dasper HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews AlternativeSplicing, Coverage, RNASeq, Sequencing, Software, Transcriptomics
Version 1.2.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
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
System Requirements
URL https://github.com/dzhang32/dasper
Bug Reports https://support.bioconductor.org/t/dasper
See More
Suggests BiocStyle, covr, testthat, GenomicState, ggplot2, ggpubr, ggrepel, grid, knitcitations, knitr, recount, rmarkdown, sessioninfo, rtracklayer, tibble
Linking To
Enhances
Depends On Me
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Build Report Build Report

Package Archives

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

Source Package dasper_1.2.0.tar.gz
Windows Binary dasper_1.2.0.zip
macOS 10.13 (High Sierra) dasper_1.2.0.tgz
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
Old Source Packages for BioC 3.13 Source Archive