sangeranalyseR

DOI: 10.18129/B9.bioc.sangeranalyseR    

This is the development version of sangeranalyseR; to use it, please install the devel version of Bioconductor.

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

Bioconductor version: Development (3.12)

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 "4.0") and enter:

if (!requireNamespace("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")

 

HTML R Script sangeranalyseR
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews Alignment, GUI, Genetics, Preprocessing, QualityControl, SangerSeq, Sequencing, Software, Visualization
Version 0.99.28
In Bioconductor since BioC 3.12 (R-4.0)
License GPL-2
Depends R (>= 3.6.0), stringr, ape, Biostrings, DECIPHER, parallel, reshape2, phangorn, sangerseqR, gridExtra, shiny, shinydashboard, shinyjs, data.table, plotly, DT, zeallot, excelR, shinycssloaders, ggdendro, shinyWidgets, openxlsx, tools, rmarkdown, kableExtra, seqinr, BiocStyle, logger
Imports
LinkingTo
Suggests knitr, 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_0.99.28.tar.gz
Windows Binary sangeranalyseR_0.99.28.zip (32- & 64-bit)
macOS 10.13 (High Sierra) sangeranalyseR_0.99.28.tgz
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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