sangeranalyseR
This is the development version of sangeranalyseR; for the stable release version, see sangeranalyseR.
sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R
Bioconductor version: Development (3.24)
This package builds on sangerseqR to allow users to create contigs from collections of Sanger sequencing reads. It provides a wide range of options for a number of commonly-performed actions including read trimming, detecting secondary peaks, and detecting indels using a reference sequence. All parameters can be adjusted interactively either in R or in the associated Shiny applications. There is extensive online documentation, and the package can outputs detailed HTML reports, including chromatograms.
Author: Rob Lanfear <rob.lanfear at gmail.com>, Kuan-Hao Chao <ntueeb05howard at gmail.com>
Maintainer: Kuan-Hao Chao <ntueeb05howard at gmail.com>
citation("sangeranalyseR")):
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("sangeranalyseR")
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("sangeranalyseR")| sangeranalyseR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Alignment, GUI, Genetics, Preprocessing, QualityControl, SangerSeq, Sequencing, Software, Visualization |
| Version | 1.23.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 years) |
| License | GPL-2 |
| Depends | R (>= 4.0.0), stringr, ape, Biostrings, pwalign, DECIPHER, parallel, reshape2, sangerseqR, gridExtra, shiny, shinydashboard, shinyjs, data.table, plotly, DT, zeallot, excelR, shinycssloaders, ggdendro, shinyWidgets, openxlsx, tools, rmarkdown (>= 2.9), knitr (>= 1.33), seqinr, BiocStyle, logger |
| Imports | |
| System Requirements | |
| URL |
See More
| Suggests | testthat (>= 2.1.0) |
| 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 | sangeranalyseR_1.23.0.tar.gz |
| Windows Binary (x86_64) | sangeranalyseR_1.23.0.zip |
| macOS Binary (big-sur-x86_64) | sangeranalyseR_1.23.0.tgz |
| macOS Binary (sonoma-arm64) | sangeranalyseR_1.23.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/sangeranalyseR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/sangeranalyseR |
| Bioc Package Browser | https://code.bioconductor.org/browse/sangeranalyseR/ |
| Package Short Url | https://bioconductor.org/packages/sangeranalyseR/ |
| Package Downloads Report | Download Stats |