cetienn01/extractgeo

An interactive python-based datasets retriever for GEO database

Hi there! 🙋🏿‍♂️

✨ I'm Chris ✨

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👨🏿‍🔬 I am a multidisciplinary scientist working at the intersection of Biology 🧫 , Chemistry ⚗️, and Data Science 👨🏿‍💻

º º º º º

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• 🗝 I’m working on identifying novel Targets 🎯 and Biomarkers 🎲 in Hematological Malignancies 🩸 and Solid Tumors 🧱
• 🔭 I’m currently learning more about AI 🚀 with a focus on Deep Learning and Machine Learning 🤖
• 💭 Ask me about Immunology 🧬, Oncology🔬 and Chemical Biology 🧪
• 🤝 I’m looking to collaborate on interesting Bioinformatics or Cheminformatics research projects
• 🤔 I’m thinking about novel approaches to Drug Discovery 💊 and Targeted Therapy ⚡
• 💯 I am passionate about STEM Education 📚 and Social Justice 💡
• 📫 You can connect with me directly at one of the platforms listed above ⬆️

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Selected Programming Tools

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Computational Research Interests

• developing novel bioinformatics tools to investigate high-throughput genomics data to understand the mechanisms of diseases, with a particular interest in cancer
• applying computational methods to study biological processes such as protein-protein interaction and protein-ligand binding to design the next generation of cell permeable and orally bioavailable macrocyclic drugs.
• implementing machine learning algorithms to support classification and prediction of clinical outcomes using molecular features

Laboratory Research Interests

• application of genome engineering techniques and high-throughput genetic screening methods to identify biological functions of unknown genes and novel drug targets in the context of ImmunoTherapy.
• assay development and tool generation to dissect immune surveillance mechanisms and T cell signaling, and validate new immunotherapy drugs
• ...

extractgeo's Issues

help with formatting (indentation, etc..)

Although the code is not complete, I think it would be good to start keeping it in the right format.
I will upload what i have so far into a text editor and see what it looks like..
@armish take a look as well whenever you get a chance. (p.s: you will see chunks of unfinished codes, here in there, but its a work in progress) 😃

while loop isn't working correctly

The while loop in the get_GEO_files function, isn't reaching my expect ValueError statement.

Use PyInstaller to easily distribute this package

The goal is is to use PyInstaller to easily distribute this Python-based package so that urs could run the application without installing anything.

update documentation and READme file

create a good well-defined project skeleton for this package

creating a layout that will be used to build the package and produce a well-maintained software package

create a slack channel to discuss project-related topics

@armish, can we create a [personal] slack channel for this repo so we can discuss all things related to this project? It would also be nice to link the channel to the GitHub repository and include notifications options in order to get live updates and track all changes as we continue to work on this? 😃