CircSeqAlignTk
This is the development version of CircSeqAlignTk; for the stable release version, see CircSeqAlignTk.
End-to-End Analysis of Small RNA-Seq Data from Viroids
Bioconductor version: Development (3.24)
CircSeqAlignTk is a toolkit for the analysis of RNA-Seq data derived from circular genome sequences, with a primary focus on viroids, circular RNAs typically consisting of a few hundred nucleotides. The toolkit supports an end-to-end analysis pipeline, from alignment to visualization.
Author: Jianqiang Sun [cre, aut]
, Xi Fu [ctb], Wei Cao [ctb]
Maintainer: Jianqiang Sun <sun at bitdessin.dev>
citation("CircSeqAlignTk")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | 1.15.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (4 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/bitdessin/CircSeqAlignTk |
| Bug Reports | https://github.com/bitdessin/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_1.15.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | CircSeqAlignTk_1.15.0.tgz |
| macOS Binary (sonoma-arm64) | CircSeqAlignTk_1.15.0.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 |