CircSeqAlignTk

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

Bioconductor version: Release (3.20)

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 [cre, aut] , Xi Fu [ctb], Wei Cao [ctb]

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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Alignment, Sequencing, SmallRNA, Software
Version	1.8.0
In Bioconductor since	BioC 3.16 (R-4.2) (2 years)
License	MIT + file LICENSE
Depends	R (>= 4.2)
Imports	stats, tools, utils, R.utils, methods, S4Vectors, rlang, magrittr, dplyr, tidyr, ggplot2, BiocGenerics, Biostrings, IRanges, ShortRead, Rsamtools, Rbowtie2, Rhisat2, shiny, shinyFiles, shinyjs, plotly, parallel, htmltools
System Requirements
URL	https://github.com/jsun/CircSeqAlignTk
Bug Reports	https://github.com/jsun/CircSeqAlignTk/issues

Suggests	knitr, rmarkdown, testthat, BiocStyle
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	CircSeqAlignTk_1.8.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)	CircSeqAlignTk_1.8.0.tgz
macOS Binary (arm64)	CircSeqAlignTk_1.7.1.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