search

nrnb / GoogleSummerOfCode

Main documentation site for NRNB GSoC project ideas and resources
114 stars 38 forks source link

Develop a Galaxy Platform Entry for NetBoxR and a Pipeline for Processing cBioPortal Data via the NetBoxR #172

Closed cannin closed 2 years ago

cannin commented 3 years ago

Background

netboxr (https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0234669) is an R package for the automated discovery of biological process modules by network analysis.

Goal

With the netboxr R package available, the goal is to make netboxr more widely available. The Galaxy platform (https://galaxyproject.org/) is a platform to make tools more widely available. The goal would be to make netboxr available on Galaxy (https://galaxyproject.org/admin/tools/add-tool-tutorial/).

Additionally, time permitting, a secondary goal would be to process datasets from cBioPortal with netboxr (https://github.com/cBioPortal/datahub/tree/master/public) following the package vignette (https://bioconductor.org/packages/release/bioc/vignettes/netboxr/inst/doc/netboxrTutorial.html).

Getting Started

Eventually, you'll need to write a proposal. Elements of this proposal should include:

  1. Demonstrated understanding (code samples help) of what steps are involved in making a Galaxy tool
  2. Try out netboxr on different sets of data from cBioPortal given the instructions in the tutorial
Getting Help

Post issues if you encounter bugs in the tutorial here: https://github.com/mil2041/netboxr/issues

Difficulty Level 1

Navigating the documentation for the Galaxy platform may have some difficulty.

Skills

Public Repository

Potential Mentors

Augustin Luna

HarshKhilawala commented 3 years ago

@cannin I find myself interested for this project. Let me know about further steps.

cannin commented 3 years ago

@HarshKhilawala I posted more details to get you started in the description

3adityajha commented 3 years ago

Hi!! Aditya here; I would like to work on this project for GSOC 2021. I am a 2nd-year Computational Biology student from IIIT Delhi. I have experience working with R & XML. I'm basically new to open source, so even a bit of help will be really appreciated! Thanks.

cannin commented 3 years ago

@3adityajha Read the project description "Getting Started" for initial steps, then learn about Galaxy, then you need to create a proposal for intended work; see application instructions: https://nrnb.org/gsoc.html.