Graph-linked unified embedding for single-cell multi-omics data integration

Context specific and dynamic gene regulatory network reconstruction and analysis

R package to visualize gene expression data based on weighted kernel density estimation

Tutorial of single-cell RNA-ATAC multiomic sequencing data analysis

PyTorch implementation of the MIDAS algorithm for single-cell multimodal data integration (Nature Biotechnology 2024).

Accurate and fast cell marker gene identification with COSG

𝒫robabilistic modeling of RNA velocity ⬱

An unsupervised approach for the integrative analysis of single-cell multi-omics data

Python package implementing our method MatchCLOT for multimodal single-cell data integration

scNOVA : Single-Cell Nucleosome Occupancy and genetic Variation Analysis

R and MATLAB scripts for MAGICAL

scMagnify is a versatile Python toolkit for inferring and analyzing gene regulatory networks (GRNs) from single-cell multi-omic datasets

Luo Lab snmCT-seq bioinformatics pipeline for joint single-nucleus methylation & transcriptome profiles.

Single-cell eQTL mapping and causal gene regulatory network inference at high efficiency and accuracy

SCOIT is an implementation of a probabilistic tensor decomposition framework for single-cell multi-omics data integration.

Pipeline to process sc-ATAC data with pyCistopic

bioinformatics pipeline for single-nucleus methylation & chromatin conformation capture assay (sn-m3C-seq)

Code and guides for the SCRGOT Coder Upgrade single cell analysis workshop

Containerized workflow for single cell detection of loss of Y chromosome and other mosaic chromosomal alterations in chronic kidney disease