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

Bioconductor version: Release (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 [cre, aut] , Xi Fu [ctb], Wei Cao [ctb]

Maintainer: Jianqiang Sun <sun at>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

CircSeqAlignTk HTML R Script
Reference Manual PDF


biocViews Alignment, Sequencing, SmallRNA, Software
Version 1.6.0
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
License MIT + file LICENSE
Depends R (>= 4.2)
Imports stats, tools, utils, R.utils, methods, S4Vectors, rlang, magrittr, dplyr, tidyr, ggplot2, BiocGenerics, Biostrings, IRanges, ShortRead, Rsamtools, Rbowtie2, Rhisat2, shiny, shinyFiles, shinyjs, plotly, parallel, htmltools
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Follow Installation instructions to use this package in your R session.

Source Package CircSeqAlignTk_1.6.0.tar.gz
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macOS Binary (x86_64) CircSeqAlignTk_1.6.0.tgz
macOS Binary (arm64) CircSeqAlignTk_1.6.0.tgz
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Source Repository (Developer Access) git clone
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