Package: scafari 1.3.0

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_1.3.0.tar.gz
scafari_1.3.0.zip(r-4.7-any)scafari_1.3.0.zip(r-4.6-any)scafari_1.3.0.zip(r-4.5-any)
scafari_1.3.0.tgz(r-4.6-any)scafari_1.3.0.tgz(r-4.5-any)
scafari_1.3.0.tar.gz(r-4.7-any)scafari_1.3.0.tar.gz(r-4.6-any)
scafari_1.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
scafari/json (API)

# Install 'scafari' in R:

install.packages('scafari', repos = c('https://bioc.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)

software shinyapps singlecell sequencing

4.30 score 2 stars 2 scripts 294 downloads 17 exports 238 dependencies

Last updated from:5d943e6af5. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	285
linux-devel	OK	714
source / vignettes	OK	576
linux-release	OK	778
macos-release	OK	741
macos-oldrel	OK	493
windows-devel	OK	438
windows-release	OK	554
windows-oldrel	OK	546
wasm-release	OK	217

Exports:annotateAmplicons annotateVariants clusterVariantSelection filterVariants h5ToSce launchScafariShiny logLogPlot normalizeReadCounts plotAmpliconDistribution plotClusterGenotype plotClusterVAF plotClusterVAFMap plotElbow plotGenotypequalityPerGenotype plotNormalizedReadCounts plotPanelUniformity plotVariantHeatmap

Dependencies:abind AnnotationDbi AnnotationFilter askpass backports base64enc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO biocmake BiocManager BiocParallel biomaRt Biostrings biovizBase bit bit64 bitops blob boot broom BSgenome bslib cachem car carData checkmate cigarillo circlize cli clue cluster codetools colorspace commonmark ComplexHeatmap corrplot cowplot cpp11 crayon crosstalk curl data.table DBI dbplyr dbscan DelayedArray dendextend Deriv dichromat digest dir.expiry doBy doParallel dplyr DT ellipse emmeans ensembldb estimability evaluate factoextra FactoMineR farver fastmap filelock flashClust fontawesome foreach forecast foreign formatR Formula fracdiff fs futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GetoptLong ggbio ggplot2 ggpubr ggrepel ggsci ggsignif GlobalOptions glue graph gridExtra gtable highr Hmisc hms htmlTable htmltools htmlwidgets httpuv httr httr2 igraph IRanges irlba isoband iterators jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice lazyeval leaps lifecycle litedown lme4 lmtest magrittr markdown MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv mime minqa modelr multcompView mvtnorm nlme nloptr nnet numDeriv openssl org.Hs.eg.db OrganismDbi otel pbkrtest pillar pkgconfig plotly plyr png polynom prettyunits progress promises ProtGenerics purrr quantreg R.methodsS3 R.oo R.utils R6 RANN rappdirs RBGL rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl Rdpack reformulas reshape2 restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstatix rstudioapi rtracklayer S4Arrays S4Vectors S7 sass scales scatterplot3d Seqinfo shape shiny shinyBS shinycssloaders shinycustomloader shinyjs showtext showtextdb SingleCellExperiment snow sourcetools SparseArray SparseM stringi stringr SummarizedExperiment survival sys sysfonts tibble tidyr tidyselect timeDate tinytex txdbmaker UCSC.utils urca utf8 VariantAnnotation vctrs viridis viridisLite waiter withr xfun XML xml2 xtable XVector yaml zoo

scafari_vignette

Rendered fromscafari_vignette.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
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 filtering	filterVariants
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 Application	launchScafariShiny
Plot a log-log plot for read counts	logLogPlot
This function normalizes the read counts contained within a `SingleCellExperiment` object.	normalizeReadCounts
Plot Distribution of Amplicons	plotAmpliconDistribution
Plot Genotype Clusters	plotClusterGenotype
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 Genotype	plotGenotypequalityPerGenotype
Plot normalized read counts	plotNormalizedReadCounts
Plot Panel Uniformity	plotPanelUniformity
Plot Variant Heatmap	plotVariantHeatmap
scafari: analyzing scDNA-seq data	scafari-package scafari