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    15 repositories

    • particle_area_count_analysis

      Public
      Quantify area and count of particles from microscopy images
      Jupyter Notebook
      •0•0•0•0•Updated Mar 4, 2026Mar 4, 2026

    • LFQ-kinase_MBR_CN

      Public
      0•0•0•0•Updated Feb 4, 2026Feb 4, 2026

    • RNAseq_expression_merge

      Public
      Merging of RNAseq transcript abundance and proteomics protein abundances, calculations of discordance and visualizations.
      0•0•0•0•Updated Jan 30, 2026Jan 30, 2026

    • Ensemble-Prediction-Pipeline-To-Identify-Neoantigens

      Public
      R
      •1•0•0•0•Updated Sep 12, 2025Sep 12, 2025

    • FPICS-Iodination-Quant

      Public
      Quantify site specific iodination using PSM level data
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Sep 9, 2025Sep 9, 2025

    • POCA_Becker

      Public
      R code used for visualization of mass spectrometry samples where protein abundance is quantified with label free–match between runs and code for multiple linear…
      0•0•0•0•Updated Sep 2, 2025Sep 2, 2025

    • ms_cpdaa_analysis

      Public
      Mass spectrometry-based chemoproteomics pipeline for analyzing electrophile selectivity and identifying chemoproteomics detected amino acids (CpDAAs)
      Python
      •
      MIT License
      •2•0•0•0•Updated Jul 17, 2025Jul 17, 2025

    • Custom-Variant-Database

      Public
      Tool to generate protein databases for custom variants
      R
      •1•0•0•0•Updated May 28, 2025May 28, 2025

    • DepMAP-Database-Generation

      Public
      Tool to generate Protein and Peptide Databases from Variant Expression data in DepMAP
      R
      •1•0•0•0•Updated May 28, 2025May 28, 2025

    • ciaa_app

      Public
      An insilico structure-based approach to identify IAA reactive cysteines.
      Jupyter Notebook
      •
      MIT License
      •0•3•2•0•Updated May 19, 2025May 19, 2025

    • CysdbAutomerge-Django

      Public
      Protein Database AutoMerging for the Backus Lab
      Python
      •1•0•0•0•Updated Apr 15, 2025Apr 15, 2025

    • chemoproteogenomics

      Public
      Generate protoegenomic search databases form variant-calling output (VCF files) and run 2-stage or multi-round FragPipe searches.
      R
      •1•0•0•0•Updated Jan 6, 2025Jan 6, 2025

    • cysloc

      Public
      Integrating chemoproteomics, subcellular localization annotations and experimental oxidation measurements to define the subcellular cysteinome and redoxome.
      Python
      •
      MIT License
      •1•0•0•0•Updated Jan 11, 2024Jan 11, 2024

    • cysdb_app

      Public
      Integrating chemoproteomics, protein structures, and functional annotations to understand the role of cysteines in the human proteome.
      Jupyter Notebook
      •
      GNU Affero General Public License v3.0
      •3•1•0•0•Updated Jun 8, 2023Jun 8, 2023

    • Cheatsheet

      Public
      Reference sheets for datascience, R, R packages, python3, PYMOL and more...
      HTML
      •3•0•0•0•Updated Apr 16, 2020Apr 16, 2020
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