Frontend visualization and incorporation of single cell data in cBioPortal

[sowmiyaa-kumar]

Background:
Researchers often seek to integrate their findings from different techniques, and by utilizing single-cell data, an extra layer of knowledge can be added to the analysis of cancer genomic datasets. cBioPortal is primarily focused on the exploration and analysis of cancer genomics data; hence, integrating single-cell data seamlessly within this framework can enhance its utility for users. This project aims to bridge this gap by enabling the integration of single-cell data visualization tools directly into cBioPortal, empowering users to explore and analyze their data in a unified environment, allowing them to interpret complex datasets more effectively. By including single-cell data on a cell-type~sample level, users can investigate the expression levels of genes between cell types within or between groups, allowing researchers to explore the heterogeneity of tumors, revealing distinct cell types and their unique gene expression profiles.

Goal:
The primary objective of this project is to develop custom tabs and visualization tools (e.g., plots) within cBioPortal and integrate dedicated single-cell data into the cBioPortal interface for a specifically tailored integrative analysis.

Approach:
The project will use front-end development technologies such as React and TypeScript to design and implement a custom single-cell tab within the cBioPortal interface. This tab will feature intuitive navigation and interactive visualization tools optimized for single-cell data analysis. In the study view, a single-cell custom tab will focus on assessing the single-cell composition through a variety of plots. We envision a boxplot showing the expression of a gene among a preselected set of samples of different cell types (see example below). Moreover, data could be split into two groups of samples (by, for example, mutated vs non-mutated samples); as such, a user can visualize the expression of a gene between the two groups on a cell type-specific level.

Need skills:
Proficiency in front-end development using React (d3js/VictoryChart) and JavaScript/TypeScript.
Familiarity with data visualization options for a user-friendly interface.

Possible mentors:
Sowmiyaa Kumar @sowmiyaa-kumar
Zeynep Karagöz @zeynepkaragoz
Mary Chapman @mlizchap

Duration of project
350 hours of work

[Vayras]

Hey! @inodb and @zeynepkaragoz I'm an open source contributor I want to partake in gsoc-2024 and I want to be a collaborator because I like the idea of providing aid to medical sciences using software development, I have been a consistent contributors recently and looking forward to start with this repository as well, Thanks

[SURAJ-SHARMA27]

Hi @sowmiyaa-kumar @inodb @zeynepkaragoz ,

My name is Suraj Sharma, and I'm currently pursuing my undergraduate degree. I believe that my tech stack aligns perfectly with this project, and I'm interested to contribute. Recently, I developed a project using the MERN stack that won in the Smart India Hackathon. Additionally, I have experience working with React Flow. My tech stack includes React.js, Node.js, Angular, Express, MongoDB, Firebase, Next.js, and Flask.

Could you please provide guidance on the next steps and how I can get started with the project?

Thank you!

[zeynepkaragoz]

Hi @SURAJ-SHARMA27 and @Vayras , thank you for your interest!
Please check this link on how to write and submit a proposal for this internship. Please share your draft proposal via a google doc with us on public cbioportal Slack so we can provide feedback. Please also remember to submit your proposal via the GSoC dashboard before the deadline.
Thanks and regards,
Zeynep & Sowmiyaa

[Vayras]

@zeynepkaragoz Thanks for the opportunity I have submitted the proposal, since the start of my open source contribution I wanted to work on projects that would help medical science and aid in cancer research and glaucoma awareness, getting a chance to work on this would mean a lot to me

[Obinnag]

I am writing to express my genuine excitement about the Front-end Development Internship opportunity focused on integrating single-cell data visualization tools into cBioPortal. Coming from a background in front-end development, I am deeply passionate about leveraging technology to contribute to advancements in cancer research, making this opportunity particularly appealing to me.

The internship's objective perfectly aligns with my skills and aspirations. My expertise in front-end technologies like React and TypeScript positions me well to design and implement custom tabs and visualization tools within the cBioPortal interface seamlessly. Additionally, my familiarity with data visualization options, such as d3js/VictoryChart, equips me to craft intuitive and user-friendly tools tailored for single-cell data analysis.

I am committed to delivering top-notch results for this project. Recognizing the importance of smooth integration and user-friendly navigation, I am confident in my ability to design a custom single-cell tab that not only meets project requirements but also enhances the overall user experience of cBioPortal.

Beyond technical skills, my passion for cancer research fuels my eagerness to contribute meaningfully to this project. I am genuinely excited about the potential impact of integrating single-cell data into cBioPortal, as it empowers researchers to delve deeper into tumor heterogeneity and decipher complex datasets effectively. Visualizing gene expression across different cell types and sample groups holds immense promise for unraveling insights into tumor behavior and composition.

Moreover, I am eager to collaborate with a team of talented individuals dedicated to advancing cancer genomics research. The opportunity to learn from experienced mentors and contribute my creativity and skills to such a transformative project is incredibly motivating for me.

Contact: [email protected]

[sowmiyaa-kumar]

Hi @Obinnag, to apply for the internship, you are required to submit a proposal by 18:00 UTC today. The guidelines are on the home page of this repo. Unfortunately, it is bit late to receive feedback but you can still submit if you'd like to.