scatac-seq

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

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

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

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).

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.

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.

A Julia package for single cell and spatial data analysis

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

A python package for chromVAR

Tools for correcting single cell barcodes for various scATAC-seq techniques and creating fragment files and spltting BAM files per cluster.

BEER: Batch EffEct Remover for single-cell data

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

The simplest, fastest software for studying gene regulation in single-cell data. Core SCENIC and SCENIC+ rewritten in Rust, with a Python API. Built and scaled with the Huang Lab at Mount Sinai.

Parse ArchR arrow files to anndata h5ad

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