CircSeqAlignTk

DOI: 10.18129/B9.bioc.CircSeqAlignTk    

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

Bioconductor version: Release (3.16)

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 "4.2") 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")

 

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PDF   Reference Manual
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Details

biocViews Alignment, Sequencing, SmallRNA, Software
Version 1.0.0
In Bioconductor since BioC 3.16 (R-4.2) (< 6 months)
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_1.0.0.tar.gz
Windows Binary
macOS Binary (x86_64) CircSeqAlignTk_1.0.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/CircSeqAlignTk
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CircSeqAlignTk
Package Short Url https://bioconductor.org/packages/CircSeqAlignTk/
Package Downloads Report Download Stats

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