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@LewisLabUCSD Lewis Lab of Systems Biology & Cell Engineering at UCSD

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    42 repositories

    • iCHO3K

      Public
      Jupyter Notebook
      •1•9•0•0•Updated Apr 22, 2026Apr 22, 2026

    • secRecon-Secretory-Pathway-Reconstruction

      Public
      Jupyter Notebook
      •0•0•0•0•Updated May 13, 2025May 13, 2025

    • GlycoMSNetworking

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Dec 20, 2024Dec 20, 2024

    • COSMIC-dFBA

      Public
      Public code for COSMIC dFBA
      MATLAB
      •
      Creative Commons Zero v1.0 Universal
      •1•0•0•0•Updated Apr 6, 2024Apr 6, 2024

    • N-Glycosylation-Markov-Models

      Public
      Cleaned-up Version
      MATLAB
      •0•3•0•0•Updated Dec 21, 2023Dec 21, 2023

    • iLipidome-website

      Public
      R
      •0•0•0•0•Updated Jul 27, 2023Jul 27, 2023

    • iLipidome

      Public
      iLipidome is a novel lipidomic data analysis framework.
      systems-biologynetwork-analysislipidomics
      systems-biologynetwork-analysislipidomics
      R
      •0•1•0•0•Updated Jul 21, 2023Jul 21, 2023

    • iLipidome-package

      Public
      HTML
      •
      Other
      •0•0•0•0•Updated Jul 21, 2023Jul 21, 2023

    • CHO96

      Public
      Code accompanying manuscript: "Deciphering the determinants of recombinant protein yield across the human secretome"
      HTML
      •1•0•0•0•Updated May 25, 2023May 25, 2023

    • secCellFie

      Public
      Expanding the CellFie tool to include the secretory pathway
      HTML
      •0•3•0•0•Updated Apr 13, 2023Apr 13, 2023

    • Mito_Trace

      Public
      Tracking cell-lineage using mutations in the mitochondrion genome.
      Jupyter Notebook
      •0•0•21•0•Updated Mar 16, 2023Mar 16, 2023

    • GlyCompare

      Public
      Comparing glycoprofiles, leveraging motif substructure arithmetic
      Jupyter Notebook
      •
      MIT License
      •2•10•4•1•Updated Jan 29, 2023Jan 29, 2023

    • GlyCompareCT

      Public
      glyCompare command line tool
      Python
      •1•3•1•0•Updated Jan 29, 2023Jan 29, 2023

    • Ligand-Receptor-Pairs

      Public
      Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.
      35•152•2•0•Updated Jan 20, 2023Jan 20, 2023

    • Celegans-cell2cell

      Public
      Analyses for cell-cell interactions in C. elegans
      Jupyter Notebook
      •2•6•0•0•Updated Nov 22, 2022Nov 22, 2022

    • CellFie

      Public
      An alternative approach to capture the breadth of cellular functions by performing a functional analysis of existing biological networks.
      MATLAB
      •
      GNU General Public License v3.0
      •5•15•0•1•Updated Oct 19, 2022Oct 19, 2022

    • autism_classifier

      Public
      Jupyter Notebook
      •2•0•0•0•Updated Sep 18, 2022Sep 18, 2022

    • StaphVaccine_BCR

      Public
      This study is for analyzing BCR data of staph vaccine (Cell Host and Microbe).
      R
      •0•0•0•0•Updated Sep 7, 2022Sep 7, 2022

    • Lectin-Sequencing

      Public
      GNU General Public License v3.0
      •0•0•0•0•Updated Dec 1, 2021Dec 1, 2021

    • CORSPOTS

      Public
      Correlative Stratification Of Proteome Trajectories
      Jupyter Notebook
      •0•0•0•0•Updated Oct 12, 2021Oct 12, 2021

    • MammalianSecretoryRecon

      Public
      Secretory Pathway Reconstruction for Human, CHO, and Mouse
      Jupyter Notebook
      •9•12•1•0•Updated Aug 24, 2021Aug 24, 2021

    • CCC-Benchmark

      Public
      Timing code for Tensor-cell2cell paper
      Python
      •0•0•0•0•Updated Jul 27, 2021Jul 27, 2021

    • cho_dna_variant_call

      Public
      Python
      •0•0•0•0•Updated Jul 21, 2021Jul 21, 2021

    • AD_secretory_pathway_figs

      Public
      R
      •0•0•0•0•Updated May 13, 2021May 13, 2021

    • PinAPL-Py

      Public
      A no hassle tool for analyzing your favorite CRISPR screen dataset!
      Python
      •11•11•1•1•Updated Apr 16, 2021Apr 16, 2021

    • AD_secretory_pathway

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Apr 11, 2021Apr 11, 2021

    • LPMO_Proteomics

      Public
      MATLAB
      •0•0•0•0•Updated Jan 14, 2021Jan 14, 2021

    • RegressionModelPipeline

      Public
      Pipeline for feature selection, interaction assessment, regression modeling and prediction assessment for 1-1000s of features
      R
      •1•4•3•0•Updated Jan 9, 2021Jan 9, 2021

    • gene-gini-matlab

      Public
      codes used for calculating and analyzing Gini genes
      MATLAB
      •0•0•0•0•Updated Dec 22, 2020Dec 22, 2020

    • HMO_GeneReaction_pred

      Public
      A flux prediction and network-based approach to resolving gene-reaction relations through transcriptomic and metabolomic data integration
      Jupyter Notebook
      •
      Apache License 2.0
      •0•1•0•0•Updated Oct 21, 2020Oct 21, 2020
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