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Main documentation site for NRNB GSoC project ideas and resources
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Implement a R Shiny Module for Network Analysis in CellMinerCDB #216

Closed cannin closed 1 year ago

cannin commented 1 year ago

Background

CellMinerCDB provides a web-based resource (https://discover.nci.nih.gov/cellminercdb/) for integrating multiple forms of pharmacological and genomic analyses, and unifying the richest cancer cell line datasets (the NCI-60, Sanger/MGH GDSC, and Broad CCLE/CTRP). CellMinerCDB enables data queries for genomics analyses, and exploration of pharmacogenomic determinants of response. It leverages overlaps of cell lines and drugs across databases to examine several biological questions. CellMinerCDB is built using R Shiny which provides a modular framework.

Goal

The goal of this project is to develop a network module for CellMinerCDB that will allow users to visualize averaged genetic profiling data on top of a curated set of pathways. Applicants should be inspired by the PathwayMapper project (https://www.pathwaymapper.org/) and its ability to visualize genomics data from cBioPortal.

How to Start

Interested applicants should:

  1. Explore the CellMinerCDB site: https://discover.nci.nih.gov/cellminercdb
  2. Download project code and set up locally and report any issues in setup: https://github.com/CBIIT/cellminercdb
  3. Review Shiny module development here: https://shiny.rstudio.com/articles/modules.html
  4. Download the cyjShiny R Shiny package for network visualization and explore demo here: https://github.com/cytoscape/cyjShiny
  5. Contact potential mentors to ask questions and write proposal for GSOC

Difficulty Level: Medium

Size and Length of Project

175 hours 12 weeks

Skills

R (essential), Javascript

Public Repository

Potential Mentors

Augustin Luna ({firstname}{last_name} AT hms.harvard.edu)

kts-desilva commented 1 year ago

Hi, may I know if this project is still available for GSOC 2023? Thanks.

khanspers commented 1 year ago

@kts-desilva: Yes it is. All open issues are available for GSoC 2023.

khanspers commented 1 year ago

This project is an active GSoC 2023 project. Closing this issue because it is no longer available for other contributors/students.