Single-Cell Integration by Non-Negative Matrix Factorization

Scissor package

A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to represent new studies without additional training.

a spatial deconvolution method based on deep learning frameworks, which converts bulk transcriptomes into spatially resolved single-cell expression profiles

CytoTRACE 2 is an interpretable AI method for predicting cellular potency and absolute developmental potential from scRNA-seq data.

Metacell - Single-cell mRNA Analysis

Assessing the purity of single cell population

TRAjectory-based Differential Expression analysis for SEQuencing data

Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data

Spatial reconstruction of dissociated single-cell data

A tool for semi-automatic cell type harmonization and integration

List of software/websites/databases/other stuff for genome engineering

A tool for detecting somatic variants in single cell data

Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics

Inferring cell-cell interactions from pseudotime ordering of scRNA-Seq data

DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map the cell transcriptome as a function of its environment.

Difference in Intercellular Communication from scRNA-seq data

Multiview Intercellular SpaTial modeling framework

Collection of computational tools for cell-cell communication inference for single-cell and spatially resolved omics

R client for the OmniPath web service

Learning cell communication from spatial graphs of cells

An ontology of cell types

reticulate-free single cell format conversion

A package to help convert different single-cell data formats to each other