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

Analysis Pipeline for Single Cell ATAC-seq

Papers with code for single cell related papers

Similarity Weighted Nonnegative Embedding (SWNE), a method for visualizing high dimensional datasets

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.

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

Accurate and fast cell marker gene identification with COSG

All-in-one analysis pipeline

<<------ Use SnapATAC!!

Workflow for analysis of healthy human kidney by snRNAseq and snATACseq

Co-accessibility network from single-cell ATAC-seq data. Python code, based on Cicero package (R).

Containerized workflow for analysis of human diabetic kidney disease by snRNA-seq and snATAC-seq

Scripts for sincle cell multiome analysis

Sanger Cellular Genetics single-cell ATAC-seq pipeline.

Single cell ANANSE Gene-regulatory-network analysis from Seurat objects

Single Cell Allele-Specific Analysis - Containerized tool for genotyping, phasing, mapping bias correction, and generation of single cell allele-specific counts

SCRIP(Single Cell Regulatory network Inference using ChIP-seq) is a tool for evaluating the binding enrichment of specific TR at single-cell resolution based on scATAC-seq.

PIASO: Precise Integration Analysis for Single-cell Omics

Binary Factor Analysis: a dimensionality reduction tool for noisy, high throughput single cell genomic data