sangeranalyseR
sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R
Bioconductor version: 3.23 · Package version: 1.22.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("sangeranalyseR")Details
| Maintainer | Kuan-Hao Chao <ntueeb05howard@gmail.com> |
| Author | Rob Lanfear <rob.lanfear@gmail.com>, Kuan-Hao Chao <ntueeb05howard@gmail.com> |
| License | GPL-2 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Alignment, GUI, Genetics, Preprocessing, QualityControl, SangerSeq, Sequencing, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/sangeranalyseR/ |
Citation
From within R, enter citation("sangeranalyseR"):
Rob Lanfear, Kuan-Hao Chao. sangeranalyseR: sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R. doi:10.18129/B9.bioc.sangeranalyseR, R package version 1.22.0, https://bioconductor.org/packages/sangeranalyseR.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | sangeranalyseR_1.22.0.tar.gz |
| Windows binary (x86_64) | sangeranalyseR_1.22.0.zip |
| macOS binary (arm64) | sangeranalyseR_1.22.0.tgz |
| macOS binary (x86_64) | sangeranalyseR_1.22.0.tgz |
Dependencies
Depends: R (>= 4.0.0), stringr, ape, Biostrings, pwalign, DECIPHER, parallel, reshape2, 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
Suggests: testthat (>= 2.1.0)