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.

 

 

COMPUTATIONAL ANALYSIS:

 

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. (2021). NucPosDB: a database of nucleosome positioning in vivo and nucleosomics of cell-free DNA. bioRxiv 2021.11.24.469884; doi: 10.1101/2021.11.24.469884