Bioconductor version: Release (3.17)
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 [aut, cre] , Xi Fu [aut], Wei Cao [aut]
Maintainer: Jianqiang Sun <sun at biunit.dev>
Citation (from within R,
enter citation("CircSeqAlignTk")
):
To install this package, start R (version "4.3") 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.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("CircSeqAlignTk")
HTML | R Script | CircSeqAlignTk |
Reference Manual | ||
Text | NEWS | |
Text | LICENSE |
biocViews | Alignment, Sequencing, SmallRNA, Software |
Version | 1.2.0 |
In Bioconductor since | BioC 3.16 (R-4.2) (1 year) |
License | MIT + file LICENSE |
Depends | R (>= 4.2) |
Imports | stats, tools, utils, methods, S4Vectors, rlang, magrittr, dplyr, tidyr, ggplot2, BiocGenerics, Biostrings, IRanges, ShortRead, Rsamtools, Rbowtie2, Rhisat2 |
LinkingTo | |
Suggests | knitr, rmarkdown, testthat, R.utils, BiocStyle |
SystemRequirements | |
Enhances | |
URL | https://github.com/jsun/CircSeqAlignTk |
BugReports | https://github.com/jsun/CircSeqAlignTk/issues |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | CircSeqAlignTk_1.2.0.tar.gz |
Windows Binary | |
macOS Binary (x86_64) | CircSeqAlignTk_1.2.0.tgz |
macOS Binary (arm64) | CircSeqAlignTk_1.2.0.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 |
Old Source Packages for BioC 3.17 | Source Archive |
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