single-cell-atac-seq

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

Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome

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

Workflow for analysis of healthy human kidney by snRNAseq and snATACseq

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

Scripts for sincle cell multiome analysis

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

graph-based cell type annotation toolkit for single-cell RNA-seq, ATAC-seq, and spatial omics

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

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

scRNA-seq and scATAC-seq utilities

Analyzing chromatin accessibility data in R

Single-cell ATAC-seq analysis of human brain cortex cells using ArchR, Harmony, motif analysis and peak-to-gene linkage.

scATAC-seq pipeline mapping mucosal immunity and host-microbe crosstalk. Profiles physical chromatin accessibility of Trm cells (Itgae/CD103) and Secretory IgA Plasma cells (Igj) to decode intestinal defense mechanisms.

A R Shiny App for single-cell analysis