mutscan

Preprocessing and Analysis of Deep Mutational Scanning Data

Bioconductor version: 3.23 · Package version: 1.2.0

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.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("mutscan")

Details

Maintainer	Charlotte Soneson <charlottesoneson@gmail.com>
Author	Charlotte Soneson [aut, cre] (ORCID: <https://orcid.org/0000-0003-3833-2169>), Michael Stadler [aut] (ORCID: <https://orcid.org/0000-0002-2269-4934>), Friedrich Miescher Institute for Biomedical Research [cph]
License	MIT + file LICENSE
URL	https://github.com/fmicompbio/mutscan
Bug Reports	https://github.com/fmicompbio/mutscan/issues
System Requirements	GNU make
Downloads rank	140
Source branch	RELEASE_3_23
biocViews	GeneticVariability, GenomicVariation, Preprocessing, Software

Documentation

Multiplexed assays of variant effect analysis with mutscan

Download

Source package

Dependencies

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

LinkingTo: Rcpp

Suggests: testthat (>= 3.0.0), BiocStyle, knitr, Biostrings, pwalign, plotly, scattermore, BiocManager