WhoIsJack
Systems biologist studying the principles of self-organization at the interface of cell and developmental biology.
University College LondonLondon, United Kingdom
WhoIsJack's Stars
awesomedata/awesome-public-datasets
A topic-centric list of HQ open datasets.
ManimCommunity/manim
A community-maintained Python framework for creating mathematical animations.
keplergl/kepler.gl
Kepler.gl is a powerful open source geospatial analysis tool for large-scale data sets.
google/latexify_py
A library to generate LaTeX expression from Python code.
gnebbia/kb
A minimalist command line knowledge base manager
jasonwebb/morphogenesis-resources
Resources on the topic of digital morphogenesis (creating form with code). Includes links to major articles, code repos, creative projects, books, software, and more.
scverse/scanpy
Single-cell analysis in Python. Scales to >1M cells.
uber/orbit
A Python package for Bayesian forecasting with object-oriented design and probabilistic models under the hood.
JustGlowing/minisom
:red_circle: MiniSom is a minimalistic implementation of the Self Organizing Maps
theislab/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"
MouseLand/cellpose
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
AllenDowney/ModSimPy
Text and supporting code for Modeling and Simulation in Python
scverse/anndata
Annotated data.
cvxgrp/pymde
Minimum-distortion embedding with PyTorch
kinnala/scikit-fem
Simple finite element assemblers
jupyter-widgets-contrib/ipygany
3-D Scientific Visualization in the Jupyter Notebook
scverse/squidpy
Spatial Single Cell Analysis in Python
aertslab/pySCENIC
pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
theislab/scvelo
RNA Velocity generalized through dynamical modeling
webermarcolivier/statannot
add statistical annotations (pvalue significance) on an existing boxplot generated by seaborn boxplot
theislab/cellrank
CellRank: dynamics from multi-view single-cell data
cytoscape/ipycytoscape
A Cytoscape Jupyter widget
brianhie/scanorama
Panoramic stitching of single cell data
dpeerlab/Palantir
Single cell trajectory detection
BiAPoL/Bio-image_Analysis_with_Python
Lecture materials "Bio-image analysis, biostatistics, programming and machine learning for computational biology" at the Center of Molecular and Cellular Bioengineering (CMCB) / University of Technology, TU Dresden
KevinMenden/scaden
Deep Learning based cell composition analysis with Scaden.
LouisFaure/scFates
a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.
DanuserLab/u-integrate
Pipeline for inference of Granger-causal relations in molecular systems to study actin regulation in lamellipodia
mmarinriera/miniyalla-py
Python implementation of some of the agent based cell models of yalla (https://github.com/germannp/yalla)
manerotoni/mypic