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1
From reads to insight: a hitchhiker's guide to ATAC-seq data analysis
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-1929-3
2
Chromatin accessibility profiling by ATAC-seq | Nature Protocols
https://www.nature.com/articles/s41596-022-00692-9
3
Complete Guide to Understanding and Using ATAC-Seq - Active Motif
https://www.activemotif.com/blog-atac-seq
4
ATAC-Seq data analysis - Galaxy Training!
https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/atac-seq/tutorial.html
5
How to Interpret ATAC-Seq Data - CD Genomics
https://www.cd-genomics.com/resource-how-to-interpret-atac-seq-data.html
6
ATAC-seq — Epigenomics Workshop 2025 1 documentation
https://nbis-workshop-epigenomics.readthedocs.io/en/latest/content/tutorials/ATACseq/lab-atacseq-bulk.html
8
Analytical Approaches for ATAC-seq Data Analysis - PMC
https://pmc.ncbi.nlm.nih.gov/articles/PMC8191135/
9
Chapter 16 ATAC-Seq | Choosing Genomics Tools
https://hutchdatascience.org/Choosing_Genomics_Tools/atac-seq-1.html
11
Assessment of computational methods for the analysis of single-cell ...
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1854-5
13
Comparison of differential accessibility analysis strategies for ATAC ...
https://www.nature.com/articles/s41598-020-66998-4
14
ATAC-Seq | GENEWIZ from Azenta
https://www.genewiz.com/public/services/next-generation-sequencing/epigenomics/atac-seq
15
ATAC-Seq for Chromatin Accessibility Analysis - Illumina
https://www.illumina.com/techniques/multiomics/epigenetics/atac-seq-chromatin-accessibility.html
16
Single-cell ATAC sequencing analysis: From data preprocessing to ...
https://www.sciencedirect.com/science/article/pii/S2001037020303019
17
CloudATAC: a cloud-based framework for ATAC-Seq data analysis
https://academic.oup.com/bib/article/25/Supplement_1/bbae090/7628554
18
ATAC-seq — Epigenomics Workshop 2025 1 documentation
https://nbis-workshop-epigenomics.readthedocs.io/en/latest/content/tutorials/atacseq_tutorials.html
19
ATAC-Seq Services - End-to-End Open Chromatin Analysis Service
https://www.activemotif.com/catalog/1233/atac-seq-service
21
ATACSeq Data Analysis - CRCD User Manual
https://crc-pages.pitt.edu/user-manual/advanced-genomics-support/ATACSeq-data-analysis/
22
ATAC Sequencing Analysis: A Helpful Guide | NanoCellect
https://nanocellect.com/blog/atac-sequencing-analysis-a-helpful-guide/
24
Review and Evaluate the Bioinformatics Analysis Strategies of ATAC ...
https://academic.oup.com/gpb/article/22/3/qzae054/7718663
25
[PDF] ATAC-seq analysis - BaRC
http://barc.wi.mit.edu/education/hot_topics/ATACseq_2024/ATACseq2024.pdf
26
ATAC-Seq: QC, peak calling, differential accessibility
https://ivanek.github.io/analysisOfGenomicsDataWithR/12_ATACSeq_html.html
27
GTN Video: ATAC-Seq data analysis - Gallantries
https://gallantries.github.io/video-library/sessions/epigenetics/atac-seq/
28
ATAC-Seq Analysis - BD Rhapsody™ Sequence Analysis Pipeline 2.3
https://bd-rhapsody-bioinfo-docs.genomics.bd.com/steps/steps_atac.html
29
Understand Single Cell ATAC-Seq Data Analysis - Broad Institute
https://www.broadinstitute.org/videos/understand-single-cell-atac-seq-data-analysis
31
The Single Cell ATAC-Seq Analysis algorithm
https://resources.qiagenbioinformatics.com/manuals/clcsinglecellanalysis/2500/index.php?manual=_Single_Cell_ATAC_Seq_Analysis_algorithm.html
32
Analytical Approaches for ATAC‐seq Data Analysis - Current Protocols
https://currentprotocols.onlinelibrary.wiley.com/doi/10.1002/cphg.101
33
A Simple Demonstration of ATAC-seq Data Analysis - Fonseca Lab
https://fonseca.lab.mcgill.ca/resources/20220810_ATAC_Analysis_Demo/guide.html
35
Best practices for the ATAC-seq assay and its data analysis
https://www.sciencedirect.com/science/article/pii/B9780128172186000164
36
Comprehensive Guide to ATAC-seq Data Analysis
https://bioinformaticamente.com/2025/01/01/comprehensive-guide-to-atac-seq-data-analysis/
38
ATAC-seq analysis in R - scvi-tools
https://docs.scvi-tools.org/en/stable/tutorials/notebooks/atac/peakvi_in_R.html
39
ATAC Sequencing | NYU Langone Health
https://med.nyu.edu/research/scientific-cores-shared-resources/applied-bioinformatics-laboratories/services/atac-sequencing
40
Pluto Bio • Automated ATAC-seq analysis platform | Assay Supported
https://pluto.bio/product/assay/atac-seq-experiment
41
[PDF] ChIP-seq and ATAC-seq - Analysis of Next-Generation Sequencing ...
https://physiology.med.cornell.edu/faculty/skrabanek/lab/angsd/lecture_notes/13_lecture.pdf
42
[PDF] ATAC-seq Data Analysis - Emory Integrated Core Facilities
https://cores.emory.edu/eicc/_includes/documents/sections/resources/ATACseq_Data_Analysis_Methods-2019_0503.pdf
43
Analyze Chromatin Accessibility with ATAC-Seq - Rosalind.bio
https://www.rosalind.bio/atac-seq-analysis
44
ATAC-Seq Analysis of Accessible Chromatin: From Experimental ...
https://experiments.springernature.com/articles/10.1007/978-1-0716-2724-2_5
45
ATAC-Seq: Introduction, Features, Workflow, and Applications
https://medium.com/%40cd-genomics/atac-seq-introduction-features-workflow-and-applications-d551b2dc3981
46
A Beginner's Guide to ATAC-seq - Novogene
https://www.novogene.com/us-en/resources/blog/a-beginners-guide-to-atac-seq/
47
Intro to ATAC-Seq: Method overview and comparison to ChIP-Seq
https://www.youtube.com/watch?v=mFY1x8_dLTI
48
Bioinformatics Analysis Using ATAC-seq and RNA-seq for ... - Frontiers
https://www.frontiersin.org/journals/oncology/articles/10.3389/fonc.2021.726551/full
49
ATAC-seq: A Powerful Tool for Chromatin Analysis - Number Analytics
https://www.numberanalytics.com/blog/atac-seq-powerful-tool-chromatin-analysis
50
ATAC-Seq: Introduction, Features, Workflow, and Applications
https://rna.cd-genomics.com/resource-atac-seq-introduction-features-workflow-and-applications.html
51
How to analyze single-cell ATAC-Seq data in R - YouTube
https://www.youtube.com/watch?v=yEKZJVjc5DY&pp=0gcJCdgAo7VqN5tD
53
ATAC-seq data analysis
https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2018/ChIP/Practicals/Practical10_ATAC-seq_analysis_SS.html
54
Single Cell ATAC sequence analysis - tv.qiagenbioinformatics.com
https://tv.qiagenbioinformatics.com/video/75570217/single-cell-atac-sequence-analysis
55
ATAC-Seq: Introduction, Features, Workflow, and Applications
https://www.pharmiweb.com/article/atac-seq-introduction-features-workflow-and-applications
57
Introduction to ATAC-seq Analysis & Pipelines - Basepair
https://www.basepairtech.com/knowledge-center/introduction-to-atac-seq-analysis-pipelines/
58
ATAC-seq Analysis: Chromatin Accessibility Profiling - Galaxy IWC
https://iwc.galaxyproject.org/workflow/atacseq-main/
59
[PDF] Streamline ChIP-Seq and ATAC-Seq analysis - Illumina
https://www.illumina.com/content/dam/illumina/gcs/assembled-assets/marketing-literature/partek-flow-application-flyer-chip-seq-and-atac-seq-m-gl-03005/partek-flow-application-flyer-chip-seq-and-atac-seq-m-gl-03005.pdf
60
Bibliometric Analysis of ATAC-Seq and Its Use in Cancer Biology via ...
https://www.frontiersin.org/journals/medicine/articles/10.3389/fmed.2020.584728/full
61
How To Analyze ATAC-seq Data For Absolute Beginners Part 2
https://ngs101.com/how-to-analyze-atac-seq-data-for-absolute-beginners-part-2-differential-binding-analysis-using-diffbind/
62
ATAC-seq – Knowledge and References - Taylor & Francis
https://taylorandfrancis.com/knowledge/Medicine_and_healthcare/Physiology/ATAC-seq/
63
Introduction to single cell ATAC data analysis in R - YouTube
https://www.youtube.com/watch?v=e2396GKFMRY
66
GTN Video: ATAC-Seq data analysis - Gallantries
https://gallantries.github.io/video-library/videos/epigenetics/atac-seq/slides/
67
[Webinar] ATAC-Seq: Mapping Open Chromatin - Dr. Michael Garbati
https://www.youtube.com/watch?v=L2Kxaq9yRE4
68
How Single-Cell ATAC-Seq Works - YouTube
https://www.youtube.com/watch?v=9K5Q7oEO7ss&pp=0gcJCdgAo7VqN5tD
70
ChIP-seq and ATAC-seq - Bioinformatics Self Learning Resources
https://libguides.usc.edu/c.php?g=1024275&p=7420318
71
Analysis of ATAC-seq data | PPT - SlideShare
https://www.slideshare.net/slideshow/analysis-of-atacseq-data/76981987
73
Sign in - Google Accounts
https://sites.google.com/site/atacseqpublic/atac-seq-analysis-methods/mitochondrialblacklists-1
74
REnformer, a single-cell ATAC-seq predicting model to investigate ...
https://www.imm.ox.ac.uk/publications/2129688
77
MPG Primer: Understand Single Cell ATAC-Seq Data Analysis (2024)
https://www.youtube.com/watch?v=sUq4yTIJqvk
80
The pioneer transcription factor Zelda controls the exit from ...
https://www.science.org/doi/10.1126/sciadv.ads5743
81
Comprehensive Guide to Downstream Analysis for Single-Cell ...
https://www.youtube.com/watch?v=pRi4IEb361w
82
Next-Generation Sequencing : Standard Operating Procedures and ...
https://catalog.libraries.psu.edu/catalog/47890925
84
ASXL1 truncating mutations drive leukemic resistance to T cell attack
https://www.biorxiv.org/content/10.1101/2025.05.29.656798v2
87
Georgios K Voloudakis MD, PhD Medical Doctor at Icahn School of ...
https://www.researchgate.net/profile/Georgios-Voloudakis
90
Dr. Jason Buenrostro Discusses How ATAC-Seq Works - YouTube
https://www.youtube.com/watch?v=OjFFPIENrWQ
92
Input files to Run ATAC Sequencing Analysis ! - YouTube
https://www.youtube.com/watch?v=aDA-oU3Pb6c
93
A Brief Overview Of ATAC-seq - YouTube
https://www.youtube.com/watch?v=Gy0sjLW2dxE&pp=ygUHI3NuYXRhYw%3D%3D
95
A Comprehensive Guide to Chromatin Accessibility & Single-Cell ...
https://www.youtube.com/watch?v=C2PxV4-zdr0
96
[PDF] User Guide Lg G3 - The Wesleyan Argus
https://www.wesleyanargus.com/virtual-library/u30ONH/2361950/user__guide_lg_g3.pdf