sangeranalyseR

DOI: 10.18129/B9.bioc.sangeranalyseR  

sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	sangeranalyseR
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Alignment, GUI, Genetics, Preprocessing, QualityControl, SangerSeq, Sequencing, Software, Visualization
Version	1.8.0
In Bioconductor since	BioC 3.12 (R-4.0) (2.5 years)
License	GPL-2
Depends	R (>= 4.0.0), stringr, ape, Biostrings, DECIPHER, parallel, reshape2, phangorn, 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
LinkingTo
Suggests	testthat (>= 2.1.0)
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	sangeranalyseR_1.8.0.tar.gz
Windows Binary	sangeranalyseR_1.8.0.zip (64-bit only)
macOS Binary (x86_64)	sangeranalyseR_1.8.0.tgz
macOS Binary (arm64)	sangeranalyseR_1.8.0.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