Pinned Repositories
MAGIC
MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological datasets.
MELD
Quantifying experimental perturbations at single cell resolution
Multiscale_PHATE
Creating multi-resolution embeddings and clusters from high dimensional data
PHATE
PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.
phateR
PHATE dimensionality reduction method implemented in R
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)
SAUCIE
scprep
A collection of scripts and tools for loading, processing, and handling single cell data.
SingleCellWorkshop
TrajectoryNet
TrajectoryNet: A Dynamic Optimal Transport Network for Modeling Cellular Dynamics
Krishnaswamy Lab's Repositories
KrishnaswamyLab/MAGIC
MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological datasets.
KrishnaswamyLab/TrajectoryNet
TrajectoryNet: A Dynamic Optimal Transport Network for Modeling Cellular Dynamics
KrishnaswamyLab/SAUCIE
KrishnaswamyLab/SingleCellWorkshop
KrishnaswamyLab/phateR
PHATE dimensionality reduction method implemented in R
KrishnaswamyLab/scprep
A collection of scripts and tools for loading, processing, and handling single cell data.
KrishnaswamyLab/Multiscale_PHATE
Creating multi-resolution embeddings and clusters from high dimensional data
KrishnaswamyLab/graphtools
Tools for building and manipulating graphs in Python
KrishnaswamyLab/AAnet
Archetypal Analysis network (AAnet)
KrishnaswamyLab/DiffusionEMD
Code corresponding to the paper Diffusion Earth Mover's Distance and Distribution Embeddings
KrishnaswamyLab/MAGAN
KrishnaswamyLab/phemd
Identifying cell subpopulational differences among single-cell biospecimens
KrishnaswamyLab/CATCH
Learning cellular hierarchy from scRNAseq data
KrishnaswamyLab/CurveNet
Diffusion curvature and Hessian prediction using point samples from quadratic hypersurfaces
KrishnaswamyLab/LearnableScattering
Learnable Geometric Scattering Network
KrishnaswamyLab/GSAE
Code from 'Uncovering the Folding Landscape of RNA Secondary Structure with Deep Graph Embeddings"
KrishnaswamyLab/visualization_selection
Selecting the right tool for the job: understanding drawbacks and biases in visualization methods
KrishnaswamyLab/GSTH
KrishnaswamyLab/Condensation
Diffusion Condensation is a topologically-inspired machine learning algorithm that is used to identify populations of cells across granularities.
KrishnaswamyLab/NN-LossLandscape-PHATE
Exploring the Geometry and Topology of Neural Network Loss Landscapes
KrishnaswamyLab/scMMGAN
KrishnaswamyLab/FMGAN
KrishnaswamyLab/GRASSY-Net
KrishnaswamyLab/NeuronTransform
KrishnaswamyLab/NSCLC_pembro_sbrt
KrishnaswamyLab/Integrated_Diffusion
Integration of diffusion operators for high dimensional multimodal data analysis
KrishnaswamyLab/FlowArtist
Flow Respecting Embeddings of Directed Graphs
KrishnaswamyLab/h_phate_demo
Demonstration of Hierarchical PHATE
KrishnaswamyLab/MURAL
KrishnaswamyLab/sk_sugar
SUGAR: https://www.krishnaswamylab.org/projects/sugar