Damsel: analysis and visualisation of DamID sequencing in R

Caitlin G Page; Andrew Londsdale; Katrina A Mitchell; Jan Schröder; Kieran F Harvey; Alicia Oshlack

doi:10.1093/bioinformatics/btae695

Damsel: analysis and visualisation of DamID sequencing in R

Bioinformatics. 2024 Nov 28;40(12):btae695. doi: 10.1093/bioinformatics/btae695.

Authors

Caitlin G Page^{1

2}, Andrew Londsdale^{1

2

3}, Katrina A Mitchell^{1

2}, Jan Schröder⁴, Kieran F Harvey^{1

2

5}, Alicia Oshlack^{1

2

6}

Affiliations

¹ Peter MacCallum Cancer Centre, Melbourne, 3000, Australia.
² Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3010, Australia.
³ Murdoch Children's Research Institute, Parkville, 3052, Australia.
⁴ Computational Sciences Initiative, Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, 3000, Australia.
⁵ Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia.
⁶ School of Mathematics and Statistics, The University of Melbourne, Parkville, 3010, Australia.

Abstract

Summary: DamID sequencing is a technique to map the genome-wide interaction of a protein with DNA. Damsel is the first Bioconductor package to provide an end to end analysis for DamID sequencing data within R. Damsel performs quantification and testing of significant binding sites along with exploratory and visual analysis. Damsel produces results consistent with previous analysis approaches.

Availability and implementation: The R package Damsel is available for install through the Bioconductor project https://bioconductor.org/packages/release/bioc/html/Damsel.html and the code is available on GitHub https://github.com/Oshlack/Damsel/.

MeSH terms

Binding Sites
DNA / genetics
High-Throughput Nucleotide Sequencing / methods
Sequence Analysis, DNA* / methods
Software*

Substances

DNA

Grants and funding

APP1194467/National Health and Medical Research Council of Australia