sangeranalyseR

DOI: 10.18129/B9.bioc.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 (3.17)

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 "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("sangeranalyseR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF		Reference Manual

Details

biocViews	Alignment, GUI, Genetics, Preprocessing, QualityControl, SangerSeq, Sequencing, Software, Visualization
Version	1.9.0
In Bioconductor since	BioC 3.12 (R-4.0) (2 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
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Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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