zsteve

gWOT

Global Waddington-OT

StationaryOT

Dynamic inference from single-cell snapshots by optimal transport

locaTE.jl

Dynamical information enables inference of gene regulation at single-cell scale

mfl

Trajectory Inference via Mean-field Langevin in Path Space

OptimalTransport.jl

Optimal transport algorithms for Julia

locaTE-paper

code and data for reproducing results from locaTE paper

SONG

This Repository Contains the Source Code for the Python Implementation of Self Organizing Nebulous Growths

EMDNetworkSimplex.jl

Julia wrapper for Nicolas Bonneel's fast C++ EMD solver

ApproxBayes.jl

Approximate Bayesian Computation (ABC) algorithms for likelihood free inference in julia

Beeline

BEELINE: evaluation of algorithms for gene regulatory network inference

BoolODE

Git Repo for simulating Boolean Models

CeSpGRN

CeSpGRN: Inferring cell specific GRN using single-cell gene expression data

Discretizers.jl

A Julia package for data discretization and label maps

GeodesicSinkhorn.jl

Geodesic Sinkhorn

GRISLI

GRISLI: Gene Regulation Inference for Single-cell with LInear differential equations and Peanian kernel velocities

homepage

HyperGraphs.jl

A package to represent high-order relationships between objects of any type

InformationMeasures.jl

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

IPMeasures.jl

Implementation of Integral Probability Measures in Julia

multitrack_clonal_haematopoiesis

A multi-track landscape of haematopoiesis informed by cellular barcoding and agent-based modelling

Muon.jl

Muon for Julia

partitioned_networks

Partitioned measure networks

PBA

Population balance analysis

QROT

Manifold Learning with Sparse Regularised Optimal Transport

SCODE

SCODE : an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation

SINCERITIES

SINCERITIES is a tool for inferring gene regulatory networks from time-stamped cross-sectional single cell transcriptional expression profiles.

SpectralClustering.jl

Spectral clustering algorithms written in Julia

TENET

TENET is a tool for reconstructing gene regulatory networks from pseudo-time ordered single-cell transcriptomic data.

TensorToolbox.jl

Julia package for tensors as multidimensional arrays, with functionalty within Tucker format, Kruskal (CP) format, Hierarchical Tucker format and Tensor Train format.

tpot

Topological Optimal Transport