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mikemartinez99/README.md

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🧬 About Me

  • Research scientist at the Dartmouth Genomic Data Science Core, supporting biomedical researchers across Dartmouth and beyond.
  • Currently developing an R package for single cell preprocessing automation (stay tuned)
  • Experienced in bulk RNA-seq, single-cell (RNA/ATAC), metagenomics, and Snakemake pipeline development.
  • Passionate about reproducible pipelines, data visualization, and genomics data.
  • On a side-quest to learn Rust!

⚙️ Tool Development & Pipelines

Project Description
RGenEDA R package for streamlined, unified, and reproducible frameworks for omics exploratory data analysis
GDSCtools R package for general genomic data science utilities
miRNA and IsomiR Pipeline Snakemake workflow for miRNA and isomiR analysis
Clover-Seq Snakemake workflow for tRNA and small RNA NGS analysis
WES Pipeline Snakemake workflow for whole-exome sequencing processing and analysis
Rust Learning Journey My side-quest of learning Rust

💻 Tech Stack

Languages:
R Snakemake Bash Python Markdown Nextflow Rust

Environments, IDEs, and Ecosystems:
Pixi Conda Bioconductor SCVerse VS Code Jupyter

Version Control:
Git GitHub


Stats Top Languages

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  1. RGenEDA RGenEDA Public

    RGenEDA package for exploratory data analysis

    R 17 3

  2. Utilitiy_Scripts Utilitiy_Scripts Public

    Helpful day to day utilities

    Shell

  3. Dartmouth-Data-Analytics-Core/DAC-RNAseq-pipeline Dartmouth-Data-Analytics-Core/DAC-RNAseq-pipeline Public

    Pipeline for processing and quality control of RNA-seq data

    Python 9 4

  4. Dartmouth-Data-Analytics-Core/GDSC-Pixi-SOP Dartmouth-Data-Analytics-Core/GDSC-Pixi-SOP Public

    SOP for using Pixi

  5. Dartmouth-Data-Analytics-Core/GDSC-miRNAseq-analysis-pipeline Dartmouth-Data-Analytics-Core/GDSC-miRNAseq-analysis-pipeline Public

    Pipeline for processing and quality control of miRNA-seq data

    Python