Introduction | Processing Multiplexed Assays of Variant Effect data | Read composition specification | Filtering | Processing TRANS data | Processing CIS data | Processing TRANS data with primers | Combining samples | Collapsing count matrix to amino acids | Diagnostic plots | Calculating fitness scores | Scoring mutations with edgeR or limma | FAQ | Can digestFastqs process a sample where the reads are spread across multiple (pairs of) FASTQ files? | Session info
Package: mutscan 1.3.0
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:
mutscan_1.3.0.tar.gz
mutscan_1.3.0.zip(r-4.7)mutscan_1.3.0.zip(r-4.6)mutscan_1.3.0.zip(r-4.5)
mutscan_1.3.0.tgz(r-4.6-x86_64)mutscan_1.3.0.tgz(r-4.6-arm64)mutscan_1.3.0.tgz(r-4.5-x86_64)mutscan_1.3.0.tgz(r-4.5-arm64)
mutscan_1.3.0.tar.gz(r-4.7-arm64)mutscan_1.3.0.tar.gz(r-4.7-x86_64)mutscan_1.3.0.tar.gz(r-4.6-arm64)mutscan_1.3.0.tar.gz(r-4.6-x86_64)
mutscan_1.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
mutscan/json (API)
| # Install 'mutscan' in R: |
| install.packages('mutscan', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/fmicompbio/mutscan/issues
Uses libs:
On BioConductor:mutscan-1.3.0(bioc 3.24)mutscan-1.2.0(bioc 3.23)
geneticvariabilitygenomicvariationpreprocessingzlibcppopenmp
Last updated from:d0c6226d03. Checks:1 NOTE, 13 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 210 | ||
| linux-devel-arm64 | OK | 359 | ||
| linux-devel-x86_64 | OK | 477 | ||
| source / vignettes | OK | 309 | ||
| linux-release-arm64 | OK | 361 | ||
| linux-release-x86_64 | OK | 437 | ||
| macos-release-arm64 | OK | 269 | ||
| macos-release-x86_64 | OK | 686 | ||
| macos-oldrel-arm64 | OK | 305 | ||
| macos-oldrel-x86_64 | OK | 521 | ||
| windows-devel | OK | 461 | ||
| windows-release | OK | 398 | ||
| windows-oldrel | OK | 421 | ||
| wasm-release | OK | 199 |
Exports:calcNearestStringDistcalculateFitnessScorecalculateRelativeFCcollapseMutantscollapseMutantsByAAcollapseMutantsBySimilaritydigestFastqsgenerateQCReportgroupSimilarSequenceslinkMultipleVariantsplotDistributionsplotFilteringplotMeanDiffplotPairsplotTotalsplotVolcanorelabelMutPositionssummarizeExperiment
Dependencies:abindbase64encBHBiobaseBiocGenericsBiocParallelBiostringsbitopsbslibcachemclicodetoolscpp11crayoncrosstalkcsawDelayedArraydigestdplyrDTedgeRevaluatefarverfastmapfontawesomeforcatsformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesGGallyggplot2ggrepelggstatsgluegtablehighrhmshtmltoolshtmlwidgetsIRangesisobandjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalocfitmagrittrMatrixMatrixGenericsmatrixStatsmemoisemetapodmimeotelpatchworkpillarpkgconfigprettyunitsprogresspromisespurrrR6rappdirsRColorBrewerRcppRhtslibrlangrmarkdownRsamtoolsS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraystatmodstringistringrSummarizedExperimenttibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunXVectoryaml
Multiplexed assays of variant effect analysis with mutscan
Last update: 2025-08-08
Started: 2019-05-22
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 |
