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
google-deepmind/mujoco
Multi-Joint dynamics with Contact. A general purpose physics simulator.
rmcelreath/stat_rethinking_2022
Statistical Rethinking course winter 2022
hmmlearn/hmmlearn
Hidden Markov Models in Python, with scikit-learn like API
duerrsimon/bioicons
A library of free open source icons for science illustrations in biology and chemistry
scverse/scvi-tools
Deep probabilistic analysis of single-cell and spatial omics data
ANTsX/ANTsPy
A fast medical imaging analysis library in Python with algorithms for registration, segmentation, and more.
pmneila/morphsnakes
Morphological snakes for image segmentation and tracking
sbi-dev/sbi
Simulation-based inference toolkit
jasonreisman/Timeline
A tool for creating SVG timelines from simple JSON input.
cellgeni/sceasy
A package to help convert different single-cell data formats to each other
drvinceknight/Nashpy
A python library for 2 player games.
theislab/scib
Benchmarking analysis of data integration tools
spacetx/starfish
starfish: unified pipelines for image-based transcriptomics
loeweX/AmortizedCausalDiscovery
Code for the paper: Amortized Causal Discovery: Learning to Infer Causal Graphs from Time-Series Data
facebookresearch/PoincareMaps
The need to understand cell developmental processes has spawned a plethora of computational methods for discovering hierarchies from scRNAseq data. However, existing techniques are based on Euclidean geometry which is not an optimal choice for modeling complex cell trajectories with multiple branches. To overcome this fundamental representation issue we propose Poincaré maps, a method harnessing the power of hyperbolic geometry into the realm of single-cell data analysis.
bunnech/cellot
Learning Single-Cell Perturbation Responses using Neural Optimal Transport
alan-turing-institute/scivision
scivision: a framework for scientific image analysis
kevinjohncutler/omnipose
Omnipose: a high-precision solution for morphology-independent cell segmentation
Socrats/EGTTools
Toolbox for Evolutionary Game Theory.
uhlmanngroup/splinedist
SplineDist: Automated Cell Segmentation with Spline Curves
krassowski/jupyterlab-citation-manager
Citation Manager for JupyterLab using Zotero Web API
cgohlke/roifile
Read and write ImageJ ROI format
SCIInstitute/fluorender
FluoRender is an interactive rendering tool for confocal microscopy data visualization.
mimesis-inria/DeepPhysX
Interfacing AI with numerical simulation.
spatial-image/spatial-image
A multi-dimensional spatial image data structure for scientific Python.
spatial-image/multiscale-spatial-image
Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-NGFF.
uhlmanngroup/muMatch
Pipeline for putting surface meshes into correspondence
gioda/FeARLesS
4D reconstruction of developmental trajectories using spherical harmonics
Research-Support-Network/research-support-network.github.io
SergeDmi/CytosimPy-article