Skip to content
View AmirUCR's full-sized avatar
🎸
🎸
5 followers · 2 following

Achievements

Achievement: Pull Sharkx2Achievement: Arctic Code Vault Contributor

Achievements

Achievement: Pull Sharkx2Achievement: Arctic Code Vault Contributor

Highlights

  • Pro

Organizations

@ucrbioinfo

Block or report AmirUCR

Block user

Prevent this user from interacting with your repositories and sending you notifications. Learn more about blocking users.

You must be logged in to block users.

Maximum 250 characters. Please don’t include any personal information such as legal names or email addresses. Markdown is supported. This note will only be visible to you.
Report abuse

Contact GitHub support about this user’s behavior. Learn more about reporting abuse.

Report abuse
AmirUCR/README.md

Hi there! 👋

I'm Amir, a Ph.D. candidate in Computer Science at UC Riverside, based in sunny Southern California 🌴

My research focuses on computational biology, with interests in genome editing (CRISPR), algorithm design, and large-scale data analysis. I build open-source tools that help make biological data more accessible, efficient, and scalable.

🧬 Most recent projects include:

  • ALLEGRO – ultra-compact CRISPR guide library design across species
  • Agentic ALLEGRO – configure and run ALLEGRO by just describing your experiment needs in English
  • SIRIUS – efficient and optimal divergent synonymous gene design
  • FUGUE – unified genome downloader for 2,000+ fungal species
  • RNA-seq Pipeline – step-by-step comprehensive bulk RNA-seq analysis
  • MSTMap Online – performant web-server for linkage mapping, and its companion Python library

Outside the terminal, you’ll find me climbing, hiking, practicing Deutsch, or playing guitar 🎸

🔬 Let’s build tools that matter.

Pinned Loading

  1. ucrbioinfo/ALLEGRO ucrbioinfo/ALLEGRO Public

    Forked from AmirUCR/ALLEGRO

    ALLEGRO is a synthetic biology tool that designs minimal, high activity CRISPR-Cas sgRNA libraries

    Python 3

  2. Agentic-ALLEGRO Agentic-ALLEGRO Public

    Describe how you want to design your ALLEGRO CRISPR experiment, and watch it happen in real time using a Claude AI agent

    Python 1

  3. RNA-seq-Pipeline RNA-seq-Pipeline Public

    RNA-seq pipeline for bulk transcriptomics – From quality control to volcano plots

    Shell 1

  4. SIRIUS SIRIUS Public

    SIRIUS is a synthetic biology tool that, given a peptide sequence, designs n maximally divergent gene sequences

    C++ 1 1

  5. FUGUE FUGUE Public

    FUGUE is a Python data collector and preprocessing tool for ALLEGRO

    Jupyter Notebook 1

  6. MSTmap-Python MSTmap-Python Public

    A Python wrapper and standalone library for MSTmap and its web-server https://mstmap.org

    C++ 1