Deep probabilistic analysis of single-cell and spatial omics data

Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses

A tool for semi-automatic cell type classification

Single cell perturbation prediction

muon is a multimodal omics Python framework

A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing

The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell level. CPA performs OOD predictions of unseen combinations of drugs, learns interpretable embeddings, estimates dose-response curves, and provides uncertainty estimates.

A tool for semi-automatic cell type harmonization and integration

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

Cell-type Annotation for Single-cell Transcriptomics using Deep Learning with a Weighted Graph Neural Network

Doublet detection in single-cell RNA-seq data.

Demultiplexing pooled scRNA-seq data with or without genotype reference

ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format.

Single-cell Hierarchical Poisson Factorization

Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) with multiple datasets.

A tool for fast and accurate summarizing of variant calling format (VCF) files

A Snakemake workflow and MrBiomics module for easy visualization of genome browser tracks of aligned BAM files (e.g., RNA-seq, ATAC-seq, scRNA-seq, ...) powered by the wrapper gtracks for the package pyGenomeTracks, and IGV-reports.

Automatic annotation of single-cell RNA-seq data from the literature

An unofficial demultiplexing strategy for SPLiT-seq RNA-Seq data

A pipeline to identify pathogenic microorganisms from scRNA-seq raw data.