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@Emergent-Behaviors-in-Biology

Emergent Behaviors in Biology

Research group of Pankaj Mehta and collaborators.

Popular repositories

  1. mlreview_notebooks mlreview_notebooks Public

    Notebooks for "A high bias low-variance introduction to Machine Learning for physicists."

    Jupyter Notebook 63 54

  2. community-simulator community-simulator Public

    Simulate microbial community batch culture experiments.

    Jupyter Notebook 37 12

  3. scTOP scTOP Public

    A package for identifying cell phenotype from single-cell RNA-sequencing data.

    Jupyter Notebook 3 2

  4. crossfeeding-transition crossfeeding-transition Public

    Code and data to accompany Marsland et al. (2018) "Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities"

    Jupyter Notebook 2 1

  5. typical-random-ecosystems typical-random-ecosystems Public

    This is the code accompanying the manuscript: Cui, Wenping, Robert Marsland III, and Pankaj Mehta. "Diverse communities behave like typical random ecosystems." arXiv:1904.02610 (2019).

    Mathematica 2 1

  6. microbiome-patterns microbiome-patterns Public

    Scripts and data to accompany Marsland, Cui and Mehta "A minimal model for microbial biodiversity can reproduce experimentally observed ecological patterns," bioRxiv 622829 (2019)

    Jupyter Notebook 1 5

Repositories

Showing 10 of 20 repositories
  • Multi-trophic-ecosystem Public

    This is repository associated with Feng et. al mansucript.

    Mathematica 0 MIT 0 0 0 Updated Mar 18, 2024
  • scTOP Public

    A package for identifying cell phenotype from single-cell RNA-sequencing data.

    Jupyter Notebook 3 GPL-3.0 2 0 0 Updated Nov 27, 2023
  • scTOP-manuscript Public

    Code and LaTeX files for "scTOP: physics-inspired order parameters for cellular identification and visualization"

    Jupyter Notebook 0 0 0 0 Updated Jul 21, 2023
  • scTOP-PanCanAtlas Public

    scTOP analysis of Pan-Cancer Atlas

    Jupyter Notebook 0 0 0 0 Updated May 16, 2023
  • Geometry-of-Coexistence Public

    Repository of interactive visualizations for "Geometry of ecological coexistence and niche differentiation"

    Mathematica 0 0 0 0 Updated Apr 2, 2023
  • scTOP-R Public

    An R package for identifying cell phenotype from single-cell RNA-sequencing data.

    Jupyter Notebook 0 0 0 0 Updated Dec 15, 2022
  • Jupyter Notebook 1 0 0 0 Updated Sep 16, 2022
  • NESS-Topology Public

    This contains notebook associated with paper "Thermodynamic origins of topological protection in nonequilibrium stochastic systems" by Mehta and Rocks.

    Jupyter Notebook 0 MIT 1 0 0 Updated Jun 15, 2022
  • community-simulator Public

    Simulate microbial community batch culture experiments.

    Jupyter Notebook 37 MIT 12 6 1 Updated Oct 21, 2020
  • immune-svm Public

    Using a machine-learning algorithm to understand adaptive immune system dynamics

    Jupyter Notebook 0 MIT 1 0 0 Updated Aug 20, 2020

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