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CircSeqAlignTk

This is the development version of CircSeqAlignTk; for the stable release version, see CircSeqAlignTk.

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

Bioconductor version: Development (3.18)

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>

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

Installation

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

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
CircSeqAlignTk HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Alignment, Sequencing, SmallRNA, Software
Version 1.3.0
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
Linking To
Suggests knitr, rmarkdown, testthat, R.utils, BiocStyle
System Requirements
Enhances
URL https://github.com/jsun/CircSeqAlignTk
Bug Reports https://github.com/jsun/CircSeqAlignTk/issues
See More
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_1.3.0.tar.gz
Windows Binary
macOS Binary (x86_64) CircSeqAlignTk_1.3.0.tgz
macOS Binary (arm64) CircSeqAlignTk_1.3.0.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