ArticleFrontiers in genetics2018
GUAVA: A Graphical User Interface for the Analysis and Visualization of ATAC-seq Data.
Article in Frontiers in genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- ChromAcS: an automated and flexible GUI for end-to-end reproducible ATAC-seq analysis across multiple species.BMC bioinformatics · 2026Article
- Method for ATAC Sequencing Data Analysis for Understanding Chromatin Biology in Legumes.Methods in molecular biology (Clifton, N.J.) · 2026Article
- EasyKASP: a simple and fast tool for KASP primer design.BMC bioinformatics · 2025Article
- Integrated multi-omics analysis identifies features that predict human pluripotent stem cell-derived progenitor differentiation to cardiomyocytes.Journal of molecular and cellular cardiology · 2024Article
- Article
- Bibliometric review of ATAC-Seq and its application in gene expression.Briefings in bioinformatics · 2022Review
- Article
- Changes in chromatin accessibility landscape and histone H3 core acetylation during valproic acid-induced differentiation of embryonic stem cells.Epigenetics & chromatin · 2021Article
- PEPATAC: an optimized pipeline for ATAC-seq data analysis with serial alignments.NAR genomics and bioinformatics · 2021Article
- ATACdb: a comprehensive human chromatin accessibility database.Nucleic acids research · 2021Article
- Loss of CBX2 induces genome instability and senescence-associated chromosomal rearrangements.The Journal of cell biology · 2020Article
- Analytical Approaches for ATAC-seq Data Analysis.Current protocols in human genetics · 2020Article
- ATAC-seq normalization method can significantly affect differential accessibility analysis and interpretation.Epigenetics & chromatin · 2020Article
- From reads to insight: a hitchhiker's guide to ATAC-seq data analysis.Genome biology · 2020Review
- ATACgraph: Profiling Genome-Wide Chromatin Accessibility From ATAC-seq.Frontiers in genetics · 2020Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) is a powerful genomic technology that is used for the global mapping and analysis of open chromatin regions. However, for users to process and analyze such data they either have to use a number of complicated bioinformatic tools or attempt to use the currently available ATAC-seq analysis software, which are not very user friendly and lack visualization of the ATAC-seq results. Because of these issues, biologists with minimal bioinformatics background who wish to process and analyze their own ATAC-seq data by themselves will find these tasks difficult and ultimately will need to seek help from bioinformatics experts. Moreover, none of the available tools provide complete solution for ATAC-seq data analysis. Therefore, to enable non-programming researchers to analyze ATAC-seq data on their own, we developed a tool called Graphical User interface for the Analysis and Visualization of ATAC-seq data (GUAVA). GUAVA is a standalone software that provides users with a seamless solution from beginning to end including adapter trimming, read mapping, the identification and differential analysis of ATAC-seq peaks, functional annotation, and the visualization of ATAC-seq results. We believe GUAVA will be a highly useful and time-saving tool for analyzing ATAC-seq data for biologists with minimal or no bioinformatics background. Since GUAVA can also operate through command-line, it can easily be integrated into existing pipelines, thus providing flexibility to users with computational experience.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.