CompassR

Overview

We developed CompassR to support more in-depth analyses and visualizations of CRE-gene linkages. CompassR is an open source R package built upon CompassDB. CompassR can be used to analyze and visualize CRE-gene linkages in one or multiple samples, and identify TFs whose motifs are enriched in selected CREs.

Installation

Installation of required packages:

# List of additional packages to install
cran_pkgs <- c("aplot", "cowplot", "dplyr", "tidyr", "ggplot2", "ggplotify", "patchwork", "RColorBrewer", "jsonlite", "httr")

# Install missing packages
sapply(cran_pkgs, function(pkg) {
  if (!requireNamespace(pkg, quietly = TRUE)) {
    install.packages(pkg, dependencies = TRUE)
  }
})

# Install Bioconductor packages if needed
bioc_pkgs <- c("biomaRt", "GenomicRanges", "Gviz")
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(bioc_pkgs, update = TRUE, ask = FALSE)

Installation of suggested packages (optional):

# List of additional packages to install
cran_pkgs <- c("Seurat", "Signac", "ggwordcloud")

# Install missing packages
sapply(cran_pkgs, function(pkg) {
  if (!requireNamespace(pkg, quietly = TRUE)) {
    install.packages(pkg, dependencies = TRUE)
  }
})

To install the latest release of CompassR from GitHub:

if (!requireNamespace("remotes", quietly = TRUE))
    install.packages("remotes")
remotes::install_github("changxinw/CompassR")

Tutorial

In our vignettes, we provide three examples for using CompassR from tissue level, celltype level, and single-sample level.

1. Tissue level: Please go the the Myh6 Regulation in Heart for tissue-level example.
2. Celltype level: Please go the the HEY2 Regulation in Cardiomyocytes for celltype-level example.
3. Sample level: Please go the the CD79B Regulation in B cells for sample-level example.
4. Integrate your inhosue data: Learn how to integrat your inhouse data from Integrating In-house Data with Datasets in CompassDB