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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:

  • RNA-seq Pipeline – step-by-step comprehensive bulk RNA-seq analysis
  • SIRIUS – efficient and optimal divergent synonymous gene design
  • ALLEGRO – ultra-compact CRISPR guide library design across species
  • FUGUE – unified genome downloader for 2,000+ fungal species
  • 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. RNA-seq-Pipeline RNA-seq-Pipeline Public

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

    Shell 1

  2. SIRIUS SIRIUS Public

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

    C++ 1 1

  3. 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

  4. FUGUE FUGUE Public

    FUGUE is a Python data collector and preprocessing tool for ALLEGRO

    Jupyter Notebook 1

  5. MSTmap-Python MSTmap-Python Public

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

    C++ 1

  6. ucrbioinfo/deepguide_reborn ucrbioinfo/deepguide_reborn Public

    A reimplementation of the original https://github.com/dDipankar/DeepGuide by Dipankar Ranjan Baisya

    Python 1