Package: scafari 1.2.0

Sophie Wind

scafari: Analysis of scDNA-seq data

Scafari is a Shiny application designed for the analysis of single-cell DNA sequencing (scDNA-seq) data provided in .h5 file format. The analysis process is structured into the four key steps "Sequencing", "Panel", "Variants", and "Explore Variants". It supports various analyses and visualizations.

Authors:Sophie Wind [aut, cre]

scafari_1.2.0.tar.gz
scafari_1.2.0.zip(r-4.7)scafari_1.2.0.zip(r-4.6)scafari_1.2.0.zip(r-4.5)
scafari_1.2.0.tgz(r-4.6-any)scafari_1.2.0.tgz(r-4.5-any)
scafari_1.2.0.tar.gz(r-4.7-any)scafari_1.2.0.tar.gz(r-4.6-any)
scafari_1.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
scafari/json (API)
NEWS

# Install 'scafari' in R:
install.packages('scafari', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sophiewind/scafari/issues

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

softwareshinyappssinglecellsequencing

4.20 score 2 stars 2 scripts 192 downloads 17 exports 234 dependencies

Last updated from:d48a0551dd (on RELEASE_3_23). Checks:1 NOTE, 4 ERROR, 5 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE248
linux-devel-x86_64ERROR701
source / vignettesOK476
linux-release-x86_64OK629
macos-release-arm64ERROR523
macos-oldrel-arm64ERROR1360
windows-develERROR771
windows-releaseOK505
windows-oldrelOK812
wasm-releaseOK241

Exports:annotateAmpliconsannotateVariantsclusterVariantSelectionfilterVariantsh5ToScelaunchScafariShinylogLogPlotnormalizeReadCountsplotAmpliconDistributionplotClusterGenotypeplotClusterVAFplotClusterVAFMapplotElbowplotGenotypequalityPerGenotypeplotNormalizedReadCountsplotPanelUniformityplotVariantHeatmap

Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIObiocmakeBiocManagerBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobbootbroomBSgenomebslibcachemcarcarDatacheckmatecigarillocirclizecliclueclustercodetoolscolorspacecommonmarkComplexHeatmapcorrplotcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrdbscanDelayedArraydendextendDerivdichromatdigestdir.expirydoBydoParalleldplyrDTellipseemmeansensembldbestimabilityevaluatefactoextraFactoMineRfarverfastmapfilelockflashClustfontawesomeforeachforecastforeignformatRFormulafracdifffsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesGetoptLongggbioggplot2ggpubrggrepelggsciggsignifGlobalOptionsgluegraphgridExtragtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttpuvhttrhttr2igraphIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevalleapslifecyclelitedownlme4lmtestmagrittrmarkdownMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrmultcompViewmvtnormnlmenloptrnnetnumDerivopensslorg.Hs.eg.dbOrganismDbiotelpbkrtestpillarpkgconfigplotlyplyrpngpolynomprettyunitsprogresspromisesProtGenericspurrrquantregR.methodsS3R.ooR.utilsR6RANNrappdirsRBGLrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRCurlRdpackreformulasreshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstatixrstudioapirtracklayerS4ArraysS4VectorsS7sassscalesscatterplot3dSeqinfoshapeshinyshinyBSshinycssloadersshinycustomloadershinyjsSingleCellExperimentsnowsourcetoolsSparseArraySparseMstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttimeDatetinytextxdbmakerUCSC.utilsurcautf8VariantAnnotationvctrsviridisviridisLitewaiterwithrxfunXMLxml2xtableXVectoryamlzoo

scafari_vignette

Rendered fromscafari_vignette.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2025-07-24
Started: 2025-04-15

Readme and manuals

Help Manual

Help pageTopics
Function: annotateAmplicons This function takes a SingleCellExperiment object as input and annotates the stored amplicons.annotateAmplicons
Function: annotateVariants This function takes a SingleCellExperiment object as input and performs variant annotation.annotateVariants
Function: clusterVariantSelection This function takes selected variants and performs clustering on them.clusterVariantSelection
Function: filterVariants ----------- This function takes a SingleCellExperiment object as input and performs variant filteringfilterVariants
Function: h5ToSce This function takes the path of an h5 file and reads this into an object of the SingleCellExperiment class.h5ToSce
Launch Scafari Shiny ApplicationlaunchScafariShiny
Plot a log-log plot for read countslogLogPlot
This function normalizes the read counts contained within a `SingleCellExperiment` object.normalizeReadCounts
Plot Distribution of AmpliconsplotAmpliconDistribution
Plot Genotype ClustersplotClusterGenotype
plot Cluster VAF This function generates a plot to visualize variant allele frequency (VAF) in clusters based on selected variants of interest.plotClusterVAF
plot Cluster VAF Map This function generates a plot to visualize variant allele frequency (VAF) in clusters based on selected variants of interest with clusters in the background.plotClusterVAFMap
This function takes a SingleCellExperiment object and variants of interest as input and plots an elbow plot to perform k-means later.plotElbow
Plot Genotype Quality per GenotypeplotGenotypequalityPerGenotype
Plot normalized read countsplotNormalizedReadCounts
Plot Panel UniformityplotPanelUniformity
Plot Variant HeatmapplotVariantHeatmap
scafari: analyzing scDNA-seq datascafari-package scafari