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 (3.20)
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("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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Alignment, Sequencing, SmallRNA, Software |
| Version | 1.8.0 |
| 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
| 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_1.8.0.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/ |
| Package Downloads Report | Download Stats |