scafari
Analysis of scDNA-seq data
Bioconductor version: 3.23 · Package version: 1.2.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("scafari")Details
| Maintainer | Sophie Wind <sophie.wind@uni-muenster.de> |
| Author | Sophie Wind [aut, cre] (ORCID: <https://orcid.org/0009-0002-1174-8201>) |
| License | LGPL-3 |
| URL | https://github.com/sophiewind/scafari |
| Bug Reports | https://github.com/sophiewind/scafari/issues |
| Downloads rank | 360 |
| Source branch | RELEASE_3_23 |
| biocViews | Sequencing, ShinyApps, SingleCell, Software |
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | scafari_1.2.0.tar.gz |
| Windows binary (x86_64) | scafari_1.2.0.zip |
| macOS binary (arm64) | scafari_1.2.0.tgz |
| macOS binary (x86_64) | scafari_1.2.0.tgz |
Dependencies
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
Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0)