dasper
This package is for version 3.12 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: 3.12
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("dasper")):
Installation
To install this package, start R (version "4.0") 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 | ||
| NEWS | Text |
Details
| biocViews | AlternativeSplicing, Coverage, RNASeq, Sequencing, Software, Transcriptomics |
| Version | 1.0.0 |
| 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 | |
| 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 | 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 |
| 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 3.12 | Source Archive |