R package for detecting doublets in single-cell RNA sequencing data

Functions for identifying and characterizing continuous developmental trajectories in single-cell data.

R package for single cell and other data analysis using diffusion maps

A tool for detecting somatic variants in single cell data

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

Spatial Transcriptomic Analysis using Reference-Free auxiliarY deep generative modeling and Shared Histology

single-cell clustering based on alternative splicing landscapes

CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data

Construct Tumor Transition Zone Microenvironment

Accurate and fast cell marker gene identification with COSG

SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.

MetaTiME: Meta-components in Tumor immune MicroEnvironment

Predict RNA velocity through deep learning

Probabilistic Learning for mlr3

Scaling Single Cell Analysis to Millions of Cells

Analysis of cell-cell communication at single-cell resolution

A novel unsupervised batch removal framework, called iMAP, based on neural networks.

Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space

R package for Protein activity analysis of single-cell RNAseq.

QuPath - Open-source bioimage analysis for research

The integration of single cell rank-based gene set enrichment analysis

Make Interactive Complex Heatmaps

A light weight shiny app tool to enable manually selection of cells from seurat object.