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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 (3.18)

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 (from within R, enter citation("sangeranalyseR")):

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

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 PDF
NEWS Text
LICENSE Text

Details

biocViews Alignment, GUI, Genetics, Preprocessing, QualityControl, SangerSeq, Sequencing, Software, Visualization
Version 1.11.0
In Bioconductor since BioC 3.12 (R-4.0) (3 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
Linking To
Suggests testthat (>= 2.1.0)
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Package Archives

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

Source Package sangeranalyseR_1.11.0.tar.gz
Windows Binary sangeranalyseR_1.11.0.zip (64-bit only)
macOS Binary (x86_64) sangeranalyseR_1.11.0.tgz
macOS Binary (arm64) sangeranalyseR_1.11.0.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