Krishnaswamy Lab

PHATE

PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.

MELD

Quantifying experimental perturbations at single cell resolution

SAUCIE

TrajectoryNet

TrajectoryNet: A Dynamic Optimal Transport Network for Modeling Cellular Dynamics

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)

scprep

A collection of scripts and tools for loading, processing, and handling single cell data.

TPHATE

MIOFlow

phemd

Identifying cell subpopulational differences among single-cell biospecimens

PECAN

PECAN: Persistent Condensation

Cell-Dynamics-Pipeline

HeatGeo

Embedding with the Heat-geodesic dissimilarity

GeoSinkhorn

Code for the paper Geodesic Sinkhorn for Fast and Accurate Optimal Transport on Manifolds.

RiTINI

Regulatory Temporal Interaction Network Inference

CSHL_ComputationalGenomics2022

Trellis

CSHL_ComputationalGenomics2023

GEFMAP

Gene-Signal-Pattern-Analysis

Learning meaningful representations of genes

ProGSNN

spARC

Denoising spatial transcriptomics data

Directed-Hierarchical-Gene-Networks

krishnaswamy-lab-site

blis

Accompanying code for the AISTATS 2024 paper BLIS-Net: Classifying and Analyzing Signals on Graphs

COMPASS

Graph Differential Equation Neural Network

FlowArtist

Flow Respecting Embeddings of Directed Graphs

FluxBrain

pytorch implementation of FluxBrain, multimodal encoder-decoder networks

harmonic-alignment

mfcn

single-cell-parathyroid-atlas