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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 (3.19)

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 "4.4") 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 1.5.0
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
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
System Requirements
URL https://github.com/jsun/CircSeqAlignTk
Bug Reports https://github.com/jsun/CircSeqAlignTk/issues
See More
Suggests knitr, rmarkdown, testthat, R.utils, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me
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Build Report Build Report

Package Archives

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

Source Package CircSeqAlignTk_1.5.0.tar.gz
Windows Binary
macOS Binary (x86_64) CircSeqAlignTk_1.5.0.tgz
macOS Binary (arm64) CircSeqAlignTk_1.5.0.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