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Bioconductor - CircSeqAlignTk

CircSeqAlignTk

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

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

Bioconductor version: Release (3.21)

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] ORCID: 0000-0002-3438-3199 , 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 "4.5") 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")
Details biocViews Alignment, Sequencing, SmallRNA, Software Version 1.10.0 In Bioconductor since BioC 3.16 (R-4.2) (2.5 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 System Requirements URL https://github.com/jsun/CircSeqAlignTk Bug Reports https://github.com/jsun/CircSeqAlignTk/issues See More Package Archives

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

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