NucPosDB is a manually curated database reporting experimental nucleosome maps in vivo across different cell types and conditions, cell-free DNA (cfDNA) datasets in people and model organisms, processed stable-nucleosome regions, as well as software for computational analysis and modelling of nucleosome positioning and “nucleosomics” analysis for medical diagnostics.
Sequenced cell-free DNA (cfDNA) datasets
Raw and processed datasets of cfDNA from body liquids such as blood plasma, urine, cerebrospinal liquid, etc.
Experimental nucleosome maps in vivo
Datasets include MNase-seq, MNase-assisted H3 ChIP-seq, chemical mapping, etc.
Stable nucleosomes of the human genome
Genomic regions with stable nucleosome occupancy in a given condition, based on in vivo and cfDNA density maps.
Prediction of nucleosome positioning
This repository contains software tools for prediction of nucleosome positioning from DNA sequence based on biophysics or bioinformatics approaches
Analysis of in vivo nucleosome positioning
This repository currently contains software solutions for analysis of MNase-seq, chemical nucleosome mapping and other experimental techniques to map nucleosomes
Tools for analysis of sequenced cfDNA
This repository is devoted to bioinformatics tools for the basic analysis of cfDNA, such as determining mutations, copy number variations, DNA methylation and nucleosome positioning reconstruction.
*How to add: To suggest a new dataset or software for inclusion in this database please email [email protected].
**How to cite: Shtumpf M., Piroeva K.V., Agrawal S.P., Jacob D.R., Teif V.B. (2022). NucPosDB: a database of nucleosome positioning in vivo and nucleosomics of cell-free DNA. Chromosoma 131, 19-28 | open access article