CircSeqAlignTk

This is the released version of CircSeqAlignTk; for the devel version, see CircSeqAlignTk.

End-to-End Analysis of Small RNA-Seq Data from Viroids

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DOI: 10.18129/B9.bioc.CircSeqAlignTk

Bioconductor version: Release (3.22)

CircSeqAlignTk is a toolkit for the analysis of RNA-Seq data derived from circular genome sequences, with a primary focus on viroids, circular RNAs typically consisting of a few hundred nucleotides. The toolkit supports an end-to-end analysis pipeline, from alignment to visualization.

Author: Jianqiang Sun [cre, aut] ORCID iD ORCID: 0000-0002-3438-3199 , Xi Fu [ctb], Wei Cao [ctb]

Maintainer: Jianqiang Sun <sun at bitdessin.dev>

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

Installation

To install this package, start R (version "4.5") 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")

Documentation 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 1.12.0

In Bioconductor since BioC 3.16 (R-4.2) (3 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/bitdessin/CircSeqAlignTk

Bug Reports https://github.com/bitdessin/CircSeqAlignTk/issues

Suggests knitr, rmarkdown, testthat, BiocStyle

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Package Archives

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

Source Package CircSeqAlignTk_1.12.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64) CircSeqAlignTk_1.12.0.tgz

macOS Binary (arm64) CircSeqAlignTk_1.12.0.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/

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