scafari
This is the development version of scafari; to use it, please install the devel version of Bioconductor.
Analysis of scDNA-seq data
Bioconductor version: Development (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]
Maintainer: Sophie Wind <sophie.wind at uni-muenster.de>
citation("scafari")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | ||
| NEWS | Text |
Details
| biocViews | Sequencing, ShinyApps, SingleCell, Software |
| Version | 0.99.12 |
| In Bioconductor since | BioC 3.22 (R-4.5) |
| 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 |
See More
| Suggests | knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scafari_0.99.12.tar.gz |
| Windows Binary (x86_64) | scafari_0.99.12.zip |
| macOS Binary (x86_64) | scafari_0.99.12.tgz |
| macOS Binary (arm64) | scafari_0.99.12.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/ |
| Package Downloads Report | Download Stats |