CircSeqAlignTk
This is the development version of CircSeqAlignTk; for the stable release version, see CircSeqAlignTk.
A toolkit for end-to-end analysis of RNA-seq data for circular genomes
Bioconductor version: Development (3.22)
CircSeqAlignTk is an end-to-end toolkit for RNA-Seq data analysis of circular genome sequences, supporting tasks from alignment to visualization. It is primarily designed for studying viroids, which are small, circular RNAs typically composed of a few hundred nucleotides. In addition to analysis capabilities, CircSeqAlignTk provides a streamlined interface for generating synthetic RNA-Seq data that closely mimics real datasets. This functionality enables developers to benchmark alignment tools, test novel alignment algorithms, and validate new workflows. This vignette offers an overview of CircSeqAlignTk and demonstrates its usage.
Author: Jianqiang Sun [cre, aut]
, Xi Fu [ctb], Wei Cao [ctb]
Maintainer: Jianqiang Sun <sun at bitdessin.dev>
citation("CircSeqAlignTk")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Alignment, Sequencing, SmallRNA, Software |
| Version | 1.11.1 |
| 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_1.11.1.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | CircSeqAlignTk_1.11.1.tgz |
| macOS Binary (arm64) | CircSeqAlignTk_1.11.1.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 |