Analysis Pipeline for Single Cell ATAC-seq
Similarity Weighted Nonnegative Embedding (SWNE), a method for visualizing high dimensional datasets
SCP provides a comprehensive set of tools for single cell data processing and downstream analysis.
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.
All-in-one analysis pipeline
Papers with code for single cell related papers
<<------ Use SnapATAC!!
Accurate and fast cell marker gene identification with COSG
Workflow for analysis of healthy human kidney by snRNAseq and snATACseq
Tutorial of single-cell RNA-ATAC multiomic sequencing data analysis
Sanger Cellular Genetics single-cell ATAC-seq pipeline.
Scripts for sincle cell multiome analysis
Single cell ANANSE Gene-regulatory-network analysis from Seurat objects
Containerized workflow for analysis of human diabetic kidney disease by snRNA-seq and snATAC-seq
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.
Single Cell Allele-Specific Analysis - Containerized tool for genotyping, phasing, mapping bias correction, and generation of single cell allele-specific counts
Binary Factor Analysis: a dimensionality reduction tool for noisy, high throughput single cell genomic data
scripts for scRNA-Seq/scATAC-Seq
A Flexible and Robust Non-parametric Test of Exchangeability
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