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PHATE
PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.MAGIC
MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological datasets.SAUCIE
TrajectoryNet
TrajectoryNet: A Dynamic Optimal Transport Network for Modeling Cellular DynamicsSingleCellWorkshop
scprep
A collection of scripts and tools for loading, processing, and handling single cell data.ReLSO-Guided-Generative-Protein-Design-using-Regularized-Transformers
a Transformer-based neural network for generating highly optimized protein sequences called Regularized Latent Space Optimization (RELSO)Multiscale_PHATE
Creating multi-resolution embeddings and clusters from high dimensional datatravelgan
graphtools
Tools for building and manipulating graphs in PythonDiffusionEMD
Code corresponding to the paper Diffusion Earth Mover's Distance and Distribution EmbeddingsAAnet
Archetypal Analysis network (AAnet)TPHATE
MAGAN
MIOFlow
phemd
Identifying cell subpopulational differences among single-cell biospecimensPECAN
PECAN: Persistent CondensationSUGAR
Synthesis using Geometrically Aligned Random-walksCATCH
Learning cellular hierarchy from scRNAseq dataGSAE
Code from 'Uncovering the Folding Landscape of RNA Secondary Structure with Deep Graph Embeddings"HeatGeo
Embedding with the Heat-geodesic dissimilarityvisualization_selection
Selecting the right tool for the job: understanding drawbacks and biases in visualization methodsLearnableScattering
Learnable Geometric Scattering NetworkCUTS
[MICCAI 2024] CUTS: A Deep Learning and Topological Framework for Multigranular Unsupervised Medical Image SegmentationLAD
Lipschitz Anomaly Discriminatorlogicml
CurveNet
Diffusion curvature and Hessian prediction using point samples from quadratic hypersurfacesCell-Dynamics-Pipeline
scgraph
Graph-based methods for the analysis of single-cell dataImageFlowNet
GeoSinkhorn
Code for the paper Geodesic Sinkhorn for Fast and Accurate Optimal Transport on Manifolds.GSPA-manuscript-analyses
Learning meaningful representations of genesGene-Signal-Pattern-Analysis
Learning meaningful representations of genesgraph_fit
New ways of fitting a graph to vector data.pointcloud_scattering
scnn
Deep learning methods for the analysis of single-cell dataTrellis
NN-LossLandscape-PHATE
Exploring the Geometry and Topology of Neural Network Loss LandscapesCSHL_ComputationalGenomics2022
Directed-Hierarchical-Gene-Networks
scMMGAN
RiTINI
Regulatory Temporal Interaction Network InferencespARC
Denoising spatial transcriptomics dataGEFMAP
CSHL_ComputationalGenomics2023
krishnaswamy-lab-site
phate-docker
Interactive command line docker script for running PHATENSCLC_pembro_sbrt
GRASSY-Net
NeuronTransform
FMGAN
Condensation
Diffusion Condensation is a topologically-inspired machine learning algorithm that is used to identify populations of cells across granularities.Love Open Source and this site? Check out how you can help us