clementleong Goto Github PK

annotables

R data package for annotating/converting Gene IDs

biotite

A comprehensive library for computational molecular biology

cermine

Content ExtRactor and MINEr

chaste

Chaste - Cancer Heart And Soft Tissue Environment - main public repository.

circos

covasim

COVID-19 Agent-based Simulator (Covasim): a model for exploring coronavirus dynamics and interventions

de_analysis

Scripts to run differential expression analysis using DESeq2 package

emod

Source files for building the IDM EMOD disease transmission model.

hitchhikersguide-gold

The Hitchhiker's Guide to the Galaxy (Solid-Gold Edition) by Steve Meretzky and Douglas Adams (Infocom)

human_epi

Data analysis for the paper "Single cell transcriptomics of human epidermis identifies basal stem cell transition states" in Nature Communications.

idm-cms

IDM compartmental modeling software (CMS)

medium

Scripts for Medium articles

mesa

Mesa is an agent-based modeling framework in Python

metastaticcancerecmremodeling

PDE-based model of ECM remodeling and its impact on metastatic cancer migration

metastaticcancerecmremodelingcc3d

Hybrid discrete-continuum model of ECM remodeling and its impact on metastatic cancer migration

modsimpy

Text and supporting code for Modeling and Simulation in Python

nerm

pdf-title-rename

A script to batch rename PDF files based on metadata/XMP title and author

pdftitle

a utility to extract the title of a PDF article

physicell

PhysiCell: Scientist end users should use latest release! Developers please fork the development branch and submit PRs to the dev branch. Thanks!

planetfall-gold

Planetfall (Solid-Gold Edition) by Steve Meretzky (Infocom)

prince-of-persia-apple-ii

A running-jumping-swordfighting game I made on the Apple II from 1985-89

pycx

PyCX is a Python-based sample code repository for complex systems research and education.

sanbomics_scripts

scripts and notebooks from sanbomics

sbmltoodepy

A tool for creating Python implementations of SBML models.

scanpy

Single-cell analysis in Python. Scales to >1M cells.

scrna-seq

single-cell-tutorial

Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"

spqsp_io_tnbc

Code of the extended spQSP version for TNBC

synthpops

Create synthetic populations for COVID-19 epidemic analyses.