sangeranalyseR
sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R
Bioconductor version: Release (3.20)
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")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 1.16.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (4 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_1.16.0.tar.gz |
| Windows Binary (x86_64) | sangeranalyseR_1.16.0.zip (64-bit only) |
| macOS Binary (x86_64) | sangeranalyseR_1.16.0.tgz |
| macOS Binary (arm64) | sangeranalyseR_1.16.0.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 |