Function demo for geomeTriD

Authors: Jianhong Ou1
Last modified: 2025-01-24

Overview

The geomeTriD is a Bioconductor package to visualize genomic interactions along with annotation for NGS dataset such as HiC, HiChIP, PLAC-seq, ChIA-PET, and HiCAR data.

Pre-requisites

  • Basic knowledge of R syntax
  • Basic knowledge of Docker if use Docker
  • Basic knowledge of shell commands
  • A computer with internet connection

Installation

To install this package, start R and enter:

library(BiocManager)
BiocManager::install("jianhong/geomeTriD_documentation")

Or try with this repository docker image:

docker run \
  -e PASSWORD=<choose_a_password_for_rstudio> \
  -p 8787:8787 \
  ghcr.io/jianhong/geomeTriD_documentation:latest

Once running, navigate to http://localhost:8787/ and then login with rstudio:yourchosenpassword.

NOTE: Running docker that uses the password in plain text like above exposes the password to others in a multi-user system (like a shared workstation or compute node). In practice, consider using an environment variable instead of plain text to pass along passwords and other secrets in docker command lines.

If you are running M1/M2 chip, although RStudio server will not work, you still can try:

mkdir tmp4output
docker run -it \
  -v ${PWD}/tmp4output:/home/rstudio/output \
  --platform linux/x86_64 \
  ghcr.io/jianhong/geomeTriD_documentation:latest \
  bash
cd output && R

Documentation

To view documentation of geomeTriD_documentation, start R and enter:

browseVignettes("geomeTriD.documentation")

The source code for showcases are available at Fig1, Fig2 and Fig3

Contributions and Support

If you would like to contribute to this package, the standard workflow is as follows:

  1. Check that there isn’t already an issue about your idea in the jianhong/geomeTriD_documentation/issues to avoid duplicating work. If there isn’t one already, please create one so that others know you’re working on this
  2. Fork the jianhong/geomeTriD_documentation to your GitHub account
  3. Make the necessary changes / additions within your forked repository following Bioconductor contribution
  4. Use devtools::build and devtools::check to check the package work properly.
  5. Submit a Pull Request against the main branch and wait for the code to be reviewed and merged

If you’re not used to this workflow with git, you can start with some docs from GitHub or even their excellent git resources.

For further information or help, don’t hesitate to get in touch on the Bioconductor support site with tag #geomeTriD.

Reporting bug/issues

Many thanks for taking an interest in improving this package. Please report bug/issues at jianhong/geomeTriD_documentation/issues.

  1. Morgridge Institute, Madison, 53715, WI, USA.↩︎