An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.

Single-cell Transcriptome and Regulome Analysis Pipeline

muon is a multimodal omics Python framework

STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data

scPerturb: A resource and a python/R tool for single-cell perturbation data

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.

SCAVENGE is a method to optimize the inference of functional and genetic associations to specific cells at single-cell resolution.

Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).

Accurate and fast cell marker gene identification with COSG

A collection of tools to process single-cell omics datasets.

Deep learning model for single-cell inference of multi-omic profiles from a single input modality.

An R package performing object conversion from ArchRProject (ArchR) to Signac SeuratObject (Signac)

A Julia package for single cell and spatial data analysis

CREsted is a Python package for training sequence-based deep learning models on scATAC-seq data, for capturing enhancer code and for designing cell type-specific sequences.

A python package for chromVAR

Tools for correcting single cell barcodes for various scATAC-seq techniques.

BEER: Batch EffEct Remover for single-cell data

Repository to reproduce all analyses for Lareau*, Ludwig*, et al. 2020

Parse ArchR arrow files to anndata h5ad

Reconstruction of higher order chromatin from scRNA-seq and scATAC-seq