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>

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

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
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
Windows Binary
macOS Binary (x86_64) sangeranalyseR_1.9.0.tgz
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/
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