Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Video

Updated: Jul 14, 2026

Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress
05:22

Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress

Published on: July 29, 2022

damidBind: an R/Bioconductor package for differential DamID analysis and data exploration.

Owen J Marshal1

  • 1Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool St, Hobart 7000, Australia.

Bioinformatics (Oxford, England)
|July 13, 2026
PubMed
Summary

The damidBind R/Bioconductor package offers the first dedicated software for analyzing DamID data, enabling researchers to identify differential DNA binding and accessibility between cell types. This tool streamlines the analysis of genome-wide protein binding profiles for reproducible results.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same journal

FIERCE: reconstructing dynamic trajectories from the differentiation potency of single cells.

Bioinformatics (Oxford, England)·2026
Same journal

Correction to: The 2024 ISCB Innovator Award-Dr Su-In Lee.

Bioinformatics (Oxford, England)·2026
Same journal

Retraction and replacement of: A deep learning architecture for metabolic pathway prediction.

Bioinformatics (Oxford, England)·2026
Same journal

A deep learning architecture for metabolic pathway prediction.

Bioinformatics (Oxford, England)·2026
Same journal

Multi-omics network reconstruction with collaborative graphical lasso.

Bioinformatics (Oxford, England)·2026
Same journal

Faster inference of complex demographic models from large allele frequency spectra.

Bioinformatics (Oxford, England)·2026

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • DamID, Targeted DamID (TaDa), and Chromatin Accessibility TaDa (CATaDa) are popular for genome-wide DNA binding protein profiling.
  • Existing methods lack dedicated software for differential analysis of DamID data across cell types.
  • Identifying differentially bound or accessible loci is crucial for understanding cell-type-specific functions.

Purpose of the Study:

  • To introduce damidBind, an R/Bioconductor package for analyzing DamID-based genome-wide profiling data.
  • To provide a dedicated software solution for identifying differentially bound or accessible loci between cell types.
  • To enable reproducible and statistically sound workflows for DamID data analysis.

Main Methods:

  • Development of an open-source R/Bioconductor package named damidBind.

More Related Videos

Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2
10:10

Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2

Published on: September 18, 2021

Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization
03:08

Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization

Published on: October 3, 2025

Related Experiment Videos

Last Updated: Jul 14, 2026

Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress
05:22

Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress

Published on: July 29, 2022

Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2
10:10

Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2

Published on: September 18, 2021

Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization
03:08

Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization

Published on: October 3, 2025

  • Implementation of functions for analyzing processed DamID binding profiles.
  • Focus on identifying differentially bound loci in a reproducible workflow.

    • Main Results:

    • The damidBind package provides essential functions for differential analysis of DamID data.
    • It enables users to transition from raw binding profiles to identifying significant differences between cell types.
    • The package facilitates a straightforward and statistically appropriate analysis workflow.

    Conclusions:

    • damidBind addresses the need for dedicated software in DamID data analysis.
    • It empowers researchers to perform cell-type-specific differential binding and accessibility analyses.
    • The package enhances the utility and accessibility of DamID techniques in genomics research.