Signac.UIO

An interactive R Shiny application for the comprehensive analysis and visualization of single-cell chromatin accessibility data. Leveraging the power of Signac, which integrates seamlessly with the Seurat package for single-cell RNA-seq analysis, Signac.UiO offers a user-friendly platform for conducting end-to-end scATAC-seq data analysis. The application supports quality control, cell filtering, dimensionality reduction, clustering, DNA motif analysis, transcription factor footprinting, and interactive data visualization. Signac.UiO is the only web server providing a comprehensive Signac-based interface for single-cell chromatin accessibility analysis. Users can upload their data, visualize results in real time, and export analysis outcomes in multiple formats, including PDF, PNG, JPEG, CSV, and TXT. The Shiny application is additionally hosted at https://xulabgdpu.org.cn/Signac.UIO.

Local Installation (Optional)

1. Download Linkage Source Code

You can obtain the source code in either of the following ways:

• Clone the GitHub repository:

  git clone https://github.com/luoyyyy/Signac.UIO.git

  Or

• Download the ZIP file from: https://github.com/luoyyyy/Signac.UIO.
  The downloaded folder should be named Linkage-main.

2. Install Required R Packages & Run Linkage

• Manual Package Installation
  1.Open your R or RStudio environment.
  2.Install the required packages:

  install.packages(c("bslib", "shiny", "shinyjs", "shinyBS", "shinyWidgets","shinybusy", "shinycssloaders", "shinydashboard", "shinydashboardPlus","ggplot2", "plotly", "patchwork", "cowplot", "dplyr", "purrr", "plyr","stringr", "sp", "Matrix", "ggseqlogo","matrixStats", "data.table", "DT", "irlba","systemfonts", "ggforce", "scatterpie"))  
  
  if (!requireNamespace("BiocManager", quietly = TRUE))
      install.packages("BiocManager")  
      
  BiocManager::install(c("MAST", "Seurat", "Signac", "SingleR", "SingleCellExperiment","ggseqlogo","BiocFileCache","AnnotationHub","BiocFileCache",
  "SummarizedExperiment", "Biobase", "MatrixGenerics","S4Vectors", "IRanges","GenomeInfoDb", "GenomicRanges","BiocGenerics","XVector", "Biostrings", "BiocIO", "rtracklayer", "BSgenome","BSgenome.Hsapiens.UCSC.hg19","GenomicFeatures", "AnnotationDbi", "AnnotationFilter", "ensembldb","EnsDb.Hsapiens.v75", "EnsDb.Hsapiens.v86", "EnsDb.Mmusculus.v79","org.Hs.eg.db", "GO.db","BSgenome.Hsapiens.UCSC.hg38","BSgenome.Hsapiens.NCBI.GRCH38", "BSgenome.Hsapiens.UCSC.hg19","BSgenome.Hsapiens.UCSC.mm10","HDO.db","clusterProfiler", "JASPAR2020"))

  ℹ️ A complete list of packages and versions can be found in the sessionInfo file.
  3.Run the application from the directory:

  shiny::runApp("/path/to/Signac.UIO-main")

Authors

Please do not hesitate to post an issue or contact the authors :

Siwen Xu: [email protected]

Yuyan Luo : [email protected]