#

single-cell-atac-seq

Here are 38 public repositories matching this topic...

zhanghao-njmu / SCP

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

scrna-seq shiny-apps single-cell shinyapps single-cell-genomics single-cell-rna-seq single-cell-analysis single-cell-atac-seq seurat single-cell-omics scrna-seq-analysis single-cell-sequencing shiny-app scanpy scatac-seq anndata scrna-pipeline seurat-objects single-cell-pipeline

Updated Mar 11, 2026
R

r3fang / SnapATAC

Analysis Pipeline for Single Cell ATAC-seq

machine-learning-algorithms sequencing epigenetics bioinformatics-pipeline single-cell-analysis single-cell-atac-seq

Updated Apr 27, 2023
R

genecell / single-cell-papers-with-code

Papers with code for single cell related papers

reproducible-research reproducible-science scrna-seq single-cell single-cell-rna-seq single-cell-atac-seq single-cell-omics scrna-seq-analysis paper-with-code

Updated Mar 23, 2026

kharchenkolab / numbat

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

cancer-genomics single-cell phylogeny single-cell-rna-seq single-cell-analysis single-cell-atac-seq cnv-detection single-cell-omics spatial-transcriptomics lineage-tracing

Updated Feb 4, 2026
R

yanwu2014 / swne

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

bioinformatics statistical-methods data-visualization dimensionality-reduction single-cell-genomics single-cell-rna-seq nonnegative-matrix-factorization single-cell-analysis single-cell-atac-seq

Updated Aug 2, 2023
R

quadbio / scMultiome_analysis_vignette

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

bioinformatics tutorial single-cell-rna-seq single-cell-analysis single-cell-atac-seq single-cell-multiomics

Updated Apr 16, 2026

genecell / COSG

Accurate and fast cell marker gene identification with COSG

single-cell marker-genes single-cell-rna-seq single-cell-analysis single-cell-atac-seq spatial-transcriptomics single-cell-multiomics piaso

Updated Sep 4, 2026
Python

Taiji-pipeline / Taiji

All-in-one analysis pipeline

transcriptional-regulatory-network single-cell-rna-seq rna-seq-pipeline single-cell-atac-seq atac-seq-pipeline

Updated Sep 3, 2024
Haskell

cantinilab / Circe

Co-accessibility network from single-cell ATAC-seq data. Python code with AnnData, based on Cicero algorithm.

gene-regulation atac-seq graphical-lasso single-cell-atac-seq cis-regulatory-elements

Updated May 23, 2026
Python

UCSC-VLAA / EpiFoundation

Pytorch implementation of EpiFoundation

single-cell single-cell-atac-seq foundation-models

Updated Feb 25, 2025
Python

r3fang / snATAC

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

clustering bioinformatics-pipeline single-cell-genomics single-cell-analysis single-cell-atac-seq

Updated Mar 15, 2019
Python

p4rkerw / Muto_Wilson_NComm_2020

Workflow for analysis of healthy human kidney by snRNAseq and snATACseq

bioinformatics genomics kidney single-cell single-cell-rna-seq single-cell-atac-seq allele-specific-expression

Updated Mar 13, 2023
R

SUwonglab / scABC

atac-seq single-cell single-cell-atac-seq

Updated Jul 3, 2019
HTML

p4rkerw / Wilson_Muto_NComm_2022

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

kidney diabetes single-cell-rna-seq heritability allele-specific single-cell-atac-seq single-cell-sequencing ckd

Updated May 18, 2023
R

kpatel427 / multiome_analysis

Scripts for sincle cell multiome analysis

single-cell 10xgenomics single-cell-rna-seq single-cell-analysis single-cell-atac-seq seurat seurat-objects

Updated Apr 6, 2022
R

cellgeni / cellatac

Sanger Cellular Genetics single-cell ATAC-seq pipeline.

atac-seq 10x-genomics single-cell-atac-seq atac-seq-pipeline nextflow-pipeline

Updated Aug 25, 2023
Nextflow

genecell / PIASO

PIASO: Precise Integrative Analysis of Single-cell Omics

data-science bioinformatics bioinformatics-pipeline transcriptomics single-cell marker-genes single-cell-genomics single-cell-rna-seq single-cell-analysis single-cell-atac-seq spatial-transcriptomics piaso

Updated Sep 15, 2026
Python

JGASmits / AnanseSeurat

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

r single-cell single-cell-rna-seq single-cell-atac-seq seurat-objects grn-analysis

Updated Sep 9, 2026
R

swainasish / ScInfeR

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

single-cell-rna-seq single-cell-atac-seq spatial-transcriptomics cell-type-annotation

Updated Sep 10, 2026
R

xindongnov / SCRIP

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 single-cell-atac-seq

Updated Jul 2, 2024
Python

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