Feb 3, 2020 · Here, we discuss the major steps in ATAC-seq data analysis, including pre-analysis (quality check and alignment), core analysis (peak calling), and advanced analysis (peak differential analysis and annotation, motif enrichment, …

Aug 20, 2024 · In this vignette, we’ll demonstrate how to jointly analyze a single-cell dataset measuring both DNA accessibility and gene expression in the same cells using Signac and Seurat. In this vignette we’ll be using a publicly available 10x …

Dec 7, 2024 · ATAC-Seq is a powerful tool that combines the advantages of RNA-Seq and Chromatin Immunoprecipitation-Sequencing (ChIP-Seq) to explore chromatin accessibility and the structure of regulatory...

Oct 26, 2020 · Here we describe an updated and optimized protocol for ATAC-seq, called Omni-ATAC, that is applicable across a broad range of cell and tissue types. The ATAC-seq workflow has five main steps:...

This includes four classes geared toward general ATAC-seq data processing: step-by-step analysis guides, raw sequence pipelines and workflows, quality control, and peak calling tools.

ATAC-seq relies on the Tn5 transposase to cleave accessible DNA sites within chromatin. The binding of Tn5 transposase to chromatin is a stochastic event.

Jun 23, 2020 · ATAC-seq is widely used to measure chromatin accessibility and identify open chromatin regions (OCRs). OCRs usually indicate active regulatory elements in the genome and are directly...

We can integrate the gene activity matrix with annotated scRNA-seq data using scANVI. First we download the Seurat-processed PBMC 10k dataset (as in their tutorial). And we convert it to AnnData using sceasy again. Subsequently, we follow the standard scANVI workflow: pretraining with scVI then running scANVI.

Feb 26, 2025 · Assay for Transposase-Accessible Chromatin with Sequencing (ATAC-seq) is widely used for characterizing chromatin accessibility across the genome.

Feb 5, 2025 · To address this challenge, we introduce EpiFoundation, a foundation model for learning cell representations from the high-dimensional and sparse space of peaks. EpiFoundation relies on an innovative cross-modality pre-training procedure with two key technical innovations.