Package: mutscan 1.2.0

Charlotte Soneson

mutscan: Preprocessing and Analysis of Deep Mutational Scanning Data

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.

Authors:Charlotte Soneson [aut, cre], Michael Stadler [aut], Friedrich Miescher Institute for Biomedical Research [cph]

mutscan_1.2.0.tar.gz
mutscan_1.2.0.zip(r-4.7)mutscan_1.2.0.zip(r-4.6)mutscan_1.2.0.zip(r-4.5)
mutscan_1.2.0.tgz(r-4.6-x86_64)mutscan_1.2.0.tgz(r-4.6-arm64)mutscan_1.2.0.tgz(r-4.5-x86_64)mutscan_1.2.0.tgz(r-4.5-arm64)
mutscan_1.2.0.tar.gz(r-4.7-arm64)mutscan_1.2.0.tar.gz(r-4.7-x86_64)mutscan_1.2.0.tar.gz(r-4.6-arm64)mutscan_1.2.0.tar.gz(r-4.6-x86_64)
mutscan_1.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
mutscan/json (API)
NEWS

# Install 'mutscan' in R:

install.packages('mutscan', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/fmicompbio/mutscan/issues

Uses libs:

zlib– Compression library
c++– GNU Standard C++ Library v3
openmp– GCC OpenMP (GOMP) support library

On BioConductor:mutscan-1.3.0(bioc 3.24)mutscan-1.2.0(bioc 3.23)

geneticvariability genomicvariation preprocessing zlib cpp openmp

6.07 score 14 stars 14 scripts 191 downloads 18 exports 101 dependencies

Last updated from:6aa85729d6 (on RELEASE_3_23). Checks:1 NOTE, 13 OK. Indexed: no.

Target	Result	Time
bioc-checks	NOTE	191
linux-devel-arm64	OK	399
linux-devel-x86_64	OK	494
source / vignettes	OK	314
linux-release-arm64	OK	414
linux-release-x86_64	OK	452
macos-release-arm64	OK	313
macos-release-x86_64	OK	661
macos-oldrel-arm64	OK	271
macos-oldrel-x86_64	OK	780
windows-devel	OK	413
windows-release	OK	423
windows-oldrel	OK	387
wasm-release	OK	167

Exports:calcNearestStringDist calculateFitnessScore calculateRelativeFC collapseMutants collapseMutantsByAA collapseMutantsBySimilarity digestFastqs generateQCReport groupSimilarSequences linkMultipleVariants plotDistributions plotFiltering plotMeanDiff plotPairs plotTotals plotVolcano relabelMutPositions summarizeExperiment

Dependencies:abind base64enc BH Biobase BiocGenerics BiocParallel Biostrings bitops bslib cachem cli codetools cpp11 crayon crosstalk csaw DelayedArray digest dplyr DT edgeR evaluate farver fastmap fontawesome forcats formatR fs futile.logger futile.options generics GenomicRanges GGally ggplot2 ggrepel ggstats glue gtable highr hms htmltools htmlwidgets IRanges isoband jquerylib jsonlite knitr labeling lambda.r later lattice lazyeval lifecycle limma locfit magrittr Matrix MatrixGenerics matrixStats memoise metapod mime otel patchwork pillar pkgconfig prettyunits progress promises purrr R6 rappdirs RColorBrewer Rcpp Rhtslib rlang rmarkdown Rsamtools S4Arrays S4Vectors S7 sass scales Seqinfo snow SparseArray statmod stringi stringr SummarizedExperiment tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun XVector yaml

Multiplexed assays of variant effect analysis with mutscan

Charlotte Soneson and Michael Stadler

Rendered frommutscan.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2025-08-08
Started: 2019-05-22

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calculate distances to the nearest string	calcNearestStringDist
Calculate fitness scores.	calculateFitnessScore
Calculate logFCs relative to WT using edgeR	calculateRelativeFC
Collapse mutants by similarity	collapseMutants collapseMutantsByAA collapseMutantsBySimilarity
Read, filter and digest sequences from fastq file(s).	digestFastqs
Generate QC report	generateQCReport
Create a conversion table for collapsing similar sequences	groupSimilarSequences
Process an experiment with multiple variable sequences	linkMultipleVariants
Plot distribution of observed values	plotDistributions
Visualize the filtering procedure	plotFiltering
Construct an MA (mean-difference) plot	plotMeanDiff
Make pairs plot of selected assay from a SummarizedExperiment object	plotPairs
Plot the column totals of a selected assay	plotTotals
Construct a volcano plot	plotVolcano
Relabel the positions of mutations in the designated ID	relabelMutPositions
Summarize and collapse multiple mutational scanning experiments	summarizeExperiment