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Adding Multi-omics data support to ABioTrans Plus #161

Closed MoHelmy closed 3 years ago

MoHelmy commented 3 years ago

OVERVIEW

ABioTrans is a bio-statistical/informatics tool that was developed in R to analyze RNASeq gene expression data. ABioTrans Plus is the webserver of ABioTrans that analyzes RNASeq or Microarray gene expression data and performs multiple gene set and protein set analyses including gene ontology (GO), pathways enrichment and co-expression analysis. ABioTrans Plus is developed to be a one-stop server for transcriptomic data analysis, including the downstream analysis of the set of resultant differentially expressed genes (DEGs).

Focus

This project aims to develop ABioTrans Plus v3.0 which will support a wider range of high throughput omics data, namely MS-based proteomics and metabolomics data. Furthermore, developing a detailed report with the performed analysis with figures and data ready to be included in the publications.

Goals

1- Developing an input module for each of the proteomics and metabolomics data. 2- Developing the preprocessing modules for each data type. 3- Connecting the preprocessed data with the downstream biostatistical analysis e.g PCA and correlation analysis. 4- Create the analysis report generator that generates the report at the end of the analysis.

Coding Skills

R programming, Shiny, JavaScript, HTML/CSS

Acceptance Criteria

Students interested in working on this project will be asked to provide their CV and school transcript then the short-listed students will be asked to do an evaluation task that will be used for assessing their fitness for the project.

Difficulty Level 2

Public Repository

ABioTrans at GitHub

Mentors

Mohamed Helmy, Thuy Tien Bui

Our Lab website

The COMPUTATIONAL BIOLOGY AND OMICS GROUP Singapore Institute of Food and Biotechnology Innovation (SIFBI), A*STAR]

yash7520 commented 3 years ago

hello this is yash i am new to open source and passionate about contributing to this project but i am not able to understand acceptance criteria do i have to submit resume before contributing to this project

MoHelmy commented 3 years ago

@yash7520 Yes, you need to submit a CV/resume and your school transcript.

yash7520 commented 3 years ago

@MoHelmy thank you sir kindly please tell where i have to submit resume and school transcript

MoHelmy commented 3 years ago

@yash7520 to the email addresses of the mentors mentioned above.

RATED-R-SUNDRAM commented 3 years ago

Hello @MoHelmy, I am Shivam Sundaram undergraduate in computational biology, I have skills in R programming and various machine language algorithms with front end languages like HTML, CSS, and Js, I am excitedly looking forward to working on this project any guidance on how to get started will be very helpful.

RATED-R-SUNDRAM commented 3 years ago

@MoHelmy I've mailed you my resume and transcript hoping to get a word from you soon.

cryolune commented 3 years ago

Hey, @MoHelmy, I hope you are doing well. I am Akhil Kumar Jha pre-final year student from Galgotias University (India). I found this project is very interesting about my stack. I have worked on R shiny app for my project. and also I have worked on data analysis and visualization. currently, I am looking forward to contributing to open source. So suggest to me, what I can do further in this project! I love to hear from you soon!

khanspers commented 3 years ago

This is an active GSoC 2021 project. The issue will be closed for the duration of GSoC since it is no longer available to other students.