CircSeqAlignTk

DOI: 10.18129/B9.bioc.CircSeqAlignTk  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see CircSeqAlignTk.

A toolkit for end-to-end analysis of RNA-seq data for circular genomes

Bioconductor version: 3.17

CircSeqAlignTk is designed for end-to-end RNA-Seq data analysis of circular genome sequences, from alignment to visualization. It mainly targets viroids which are composed of 246-401 nt circular RNAs. In addition, CircSeqAlignTk implements a tidy interface to generate synthetic sequencing data that mimic real RNA-Seq data, allowing developers to evaluate the performance of alignment tools and workflows.

Author: Jianqiang Sun [aut, cre] , Xi Fu [aut], Wei Cao [aut]

Maintainer: Jianqiang Sun <sun at biunit.dev>

Installation

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

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

BiocManager::install("CircSeqAlignTk")

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("CircSeqAlignTk")

 

HTML	R Script	CircSeqAlignTk
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Alignment, Sequencing, SmallRNA, Software
Version	1.2.0
In Bioconductor since	BioC 3.16 (R-4.2) (1 year)
License	MIT + file LICENSE
Depends	R (>= 4.2)
Imports	stats, tools, utils, methods, S4Vectors, rlang, magrittr, dplyr, tidyr, ggplot2, BiocGenerics, Biostrings, IRanges, ShortRead, Rsamtools, Rbowtie2, Rhisat2
LinkingTo
Suggests	knitr, rmarkdown, testthat, R.utils, BiocStyle
SystemRequirements
Enhances
URL	https://github.com/jsun/CircSeqAlignTk
BugReports	https://github.com/jsun/CircSeqAlignTk/issues
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	CircSeqAlignTk_1.2.0.tar.gz
Windows Binary
macOS Binary (x86_64)	CircSeqAlignTk_1.2.0.tgz
macOS Binary (arm64)	CircSeqAlignTk_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CircSeqAlignTk
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CircSeqAlignTk
Bioc Package Browser	https://code.bioconductor.org/browse/CircSeqAlignTk/
Package Short Url	https://bioconductor.org/packages/CircSeqAlignTk/
Package Downloads Report	Download Stats