mutscan
This is the released version of mutscan; for the devel version, see mutscan.
Preprocessing and Analysis of Deep Mutational Scanning Data
Bioconductor version: Release (3.23)
Provides functionality for processing and statistical analysis of multiplexed assays of variant effect (MAVE) and similar data. The package contains functions covering the full workflow from raw FASTQ files to publication-ready visualizations. A broad range of library designs can be processed with a single, unified interface.
Author: Charlotte Soneson [aut, cre]
, Michael Stadler [aut]
, Friedrich Miescher Institute for Biomedical Research [cph]
Maintainer: Charlotte Soneson <charlottesoneson at gmail.com>
citation("mutscan")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("mutscan")
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("mutscan")| mutscan | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneticVariability, GenomicVariation, Preprocessing, Software |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (1 year) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5.0) |
| Imports | BiocGenerics, S4Vectors, methods, SummarizedExperiment, Rcpp, edgeR(>= 3.42.0), dplyr, Matrix, limma, tidyr, stats, GGally, ggplot2, tidyselect (>= 1.2.0), tibble, rlang, grDevices, csaw, rmarkdown, xfun, DT, ggrepel, IRanges, utils, DelayedArray, tools |
| System Requirements | GNU make |
| URL | https://github.com/fmicompbio/mutscan |
| Bug Reports | https://github.com/fmicompbio/mutscan/issues |
See More
| Suggests | testthat (>= 3.0.0), BiocStyle, knitr, Biostrings, pwalign, plotly, scattermore, BiocManager |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | mutscan_1.2.0.tar.gz |
| Windows Binary (x86_64) | mutscan_1.2.0.zip |
| macOS Binary (big-sur-x86_64) | mutscan_1.2.0.tgz |
| macOS Binary (sonoma-arm64) | mutscan_1.2.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/mutscan |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/mutscan |
| Bioc Package Browser | https://code.bioconductor.org/browse/mutscan/ |
| Package Short Url | https://bioconductor.org/packages/mutscan/ |
| Package Downloads Report | Download Stats |