scafari

This is the released version of scafari; for the devel version, see scafari.

Analysis of scDNA-seq data

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DOI: 10.18129/B9.bioc.scafari

Bioconductor version: Release (3.22)

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.

Author: Sophie Wind [aut, cre] ORCID iD ORCID: 0009-0002-1174-8201

Maintainer: Sophie Wind <sophie.wind at uni-muenster.de>

Citation (from within R, enter citation("scafari")):

Installation

To install this package, start R (version "4.5") and enter:


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

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("scafari")

scafari_vignette HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Sequencing, ShinyApps, SingleCell, Software

Version 1.0.0

In Bioconductor since BioC 3.22 (R-4.5) (< 6 months)

License LGPL-3

Depends R (>= 4.5.0)

Imports magrittr, shiny, shinycssloaders, DT, dplyr, waiter, ggplot2, tibble, stringr, reshape2, shinyjs, shinyBS, shinycustomloader, factoextra, markdown, plotly, ggbio, GenomicRanges, rhdf5, ComplexHeatmap, biomaRt, org.Hs.eg.db, SummarizedExperiment, SingleCellExperiment, S4Vectors, parallel, httr, jsonlite, scales, tidyr, txdbmaker, circlize, R.utils, dbscan, igraph, RANN

System Requirements

URL https://github.com/sophiewind/scafari

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

Suggests knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0)

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package scafari_1.0.0.tar.gz

Windows Binary (x86_64) scafari_1.0.0.zip (64-bit only)

macOS Binary (x86_64) scafari_1.0.0.tgz

macOS Binary (arm64) scafari_1.0.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/scafari

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scafari

Bioc Package Browser https://code.bioconductor.org/browse/scafari/

Package Short Url https://bioconductor.org/packages/scafari/

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