adamlmaclean

julia-dynsys-resources

Dynamical systems modeling in Julia with 🐜 & 🐟

AABayes.jl

Approximate Approximate Bayesian Computation

Cell-Cell-Communication

Code to accompany the paper bioRxiv: 10.1101/2021.03.31.437948.

compbio-edi

Curated summary of efforts to promote equity, diversity, and inclusion in computational biology PhD programs and societies.

covid19-review

A collaborative review of the emerging literature on diagnostics and treatments related to COVID-19

data-science-seminar

Topics in Data Science

DifferentialEquations.jl

Julia suite for high-performance solvers of differential equations

InformationMeasures.jl

Entropy, mutual information and higher order measures from information theory, with various estimators and discretisation methods.

RSoptSC

Similarity matrix optimization for cell clustering, lineage, and signaling inference

MCSTracker

ModelingMDSCs

Code for Myeloid-derived suppressor cell dynamics control outcomes in the metastatic niche

nielab.github.io

Nie Lab Website

popInfer

PyDSTool.jl

A wrapper for the PyDSTool library

RVAgene

Recurrent Variational Auto gene encoder

scEpath

a novel tool for analyzing single cell RNA-seq data

seurat

R toolkit for single cell genomics

SoCalSysBio2023

SoptSC

SOptSC for single cell data analysis

stan

Stan development repository (home page is linked below). The master branch contains the current release. The develop branch contains the latest stable development. See the Developer Process Wiki for details.

Stan.jl

Julia package to use Stan as an external program

stemcell-superhero

Interactive cell differentiation model demo

Tumor-Immune-EMT

A repository for writing this paper.

tumor-immune-emt-code

Code associated with Bergman, Karikomi, Nie, MacLean (2019). Modeling the competing effects of the immune system and EMT on tumor development.

Warne2018

Codes associated with Warne, Baker and Simpson (2018) Implementations of simulation and inference algorithms for stochastic reaction networks: from basic concepts to state-of-the-art

www.julialang.org

Julia Project website