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ann-benchmarks

Benchmarks of approximate nearest neighbor libraries in Python

awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

cytocommunity

A spatial omics data analysis tool that enables both unsupervised and supervised discovery of complex tissue cellular neighborhoods from cell phenotypes.

cytocommunity-beta_v1.1.0

cytocommunity_tutorials

cytotalk

A novel computational method for inferring cell-type-specific signaling networks using single-cell transcriptomics data for better characterization of cell-cell communication.

cytotalk_pro

diffpool

kgraph

A library for k-nearest neighbor search

ligand-receptor-pairs

Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.

opticon

A general framework for systematic and de novo identification of synergistic key regulators.

pytorch_geometric

Geometric Deep Learning Extension Library for PyTorch

seurat

R toolkit for single cell genomics

snap

Stanford Network Analysis Platform (SNAP) is a general purpose network analysis and graph mining library.

spagcn

SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network

viscello

Viscello for Visualization of Single Cell Data

weavess

A Comprehensive Survey and Experimental Comparison of Graph-based Approximate Nearest Neighbor Search