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 [aut], Kuan-Hao Chao [aut, cre]
Maintainer: Kuan-Hao Chao <ntueeb05howard at gmail.com>
citation("sangeranalyseR")):Rob Lanfear, Kuan-Hao Chao. sangeranalyseR: sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R. doi:10.18129/B9.bioc.sangeranalyseR, R package version 1.23.0, https://bioconductor.org/packages/sangeranalyseR.
Generated from the package metadata; it may differ from the package's own citation.
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")| An Introduction to 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 | file LICENSE |
| Depends | R (>= 4.0.0), Biostrings, DECIPHER, sangerseqR |
| Imports | ape, BiocGenerics, BiocParallel, S4Vectors, data.table, DT, excelR, ggdendro, grDevices, graphics, gridExtra, logger, methods, openxlsx, parallel, plotly, pwalign, Rcpp, rmarkdown (>= 2.9), seqinr, shiny, shinycssloaders, shinydashboard, shinyjs, shinyWidgets, stats, stringr, tools, utils |
| System Requirements | |
| URL | https://github.com/roblanf/sangeranalyseR |
| Bug Reports | https://github.com/roblanf/sangeranalyseR/issues |
See More
| Suggests | testthat (>= 2.1.0), withr, BiocManager, BiocStyle, knitr (>= 1.33), reshape2, zeallot |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
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 |
| Package Short Url | https://bioconductor.org/packages/sangeranalyseR/ |
| Package Downloads Report | Download Stats |