iNucs: inter-nucleosome interactions

MOTIVATION: Deciphering nucleosome–nucleosome interactions is an important step toward mesoscale description of chromatin organization but computational tools to perform such analyses are not publicly available. RESULTS: We developed iNucs, a user-friendly and efficient Python-based bioinformatics t...

Descripción completa

Detalles Bibliográficos
Autores principales: Oveisi, Mehrdad, Shukla, Manu, Seymen, Nogayhan, Ohno, Masae, Taniguchi, Yuichi, Nahata, Sunil, Loos, Remco, Mufti, Ghulam J, Allshire, Robin C, Dimitrov, Stefan, Karimi, Mohammad M
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8652021/
https://www.ncbi.nlm.nih.gov/pubmed/34623394
http://dx.doi.org/10.1093/bioinformatics/btab698
_version_ 1784611502154579968
author Oveisi, Mehrdad
Shukla, Manu
Seymen, Nogayhan
Ohno, Masae
Taniguchi, Yuichi
Nahata, Sunil
Loos, Remco
Mufti, Ghulam J
Allshire, Robin C
Dimitrov, Stefan
Karimi, Mohammad M
author_facet Oveisi, Mehrdad
Shukla, Manu
Seymen, Nogayhan
Ohno, Masae
Taniguchi, Yuichi
Nahata, Sunil
Loos, Remco
Mufti, Ghulam J
Allshire, Robin C
Dimitrov, Stefan
Karimi, Mohammad M
author_sort Oveisi, Mehrdad
collection PubMed
description MOTIVATION: Deciphering nucleosome–nucleosome interactions is an important step toward mesoscale description of chromatin organization but computational tools to perform such analyses are not publicly available. RESULTS: We developed iNucs, a user-friendly and efficient Python-based bioinformatics tool to compute and visualize nucleosome-resolved interactions using standard pairs format input generated from pairtools. AVAILABILITYAND IMPLEMENTATION: https://github.com/Karimi-Lab/inucs/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
format Online
Article
Text
id pubmed-8652021
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-86520212021-12-08 iNucs: inter-nucleosome interactions Oveisi, Mehrdad Shukla, Manu Seymen, Nogayhan Ohno, Masae Taniguchi, Yuichi Nahata, Sunil Loos, Remco Mufti, Ghulam J Allshire, Robin C Dimitrov, Stefan Karimi, Mohammad M Bioinformatics Applications Notes MOTIVATION: Deciphering nucleosome–nucleosome interactions is an important step toward mesoscale description of chromatin organization but computational tools to perform such analyses are not publicly available. RESULTS: We developed iNucs, a user-friendly and efficient Python-based bioinformatics tool to compute and visualize nucleosome-resolved interactions using standard pairs format input generated from pairtools. AVAILABILITYAND IMPLEMENTATION: https://github.com/Karimi-Lab/inucs/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2021-10-08 /pmc/articles/PMC8652021/ /pubmed/34623394 http://dx.doi.org/10.1093/bioinformatics/btab698 Text en © The Author(s) 2021. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Notes
Oveisi, Mehrdad
Shukla, Manu
Seymen, Nogayhan
Ohno, Masae
Taniguchi, Yuichi
Nahata, Sunil
Loos, Remco
Mufti, Ghulam J
Allshire, Robin C
Dimitrov, Stefan
Karimi, Mohammad M
iNucs: inter-nucleosome interactions
title iNucs: inter-nucleosome interactions
title_full iNucs: inter-nucleosome interactions
title_fullStr iNucs: inter-nucleosome interactions
title_full_unstemmed iNucs: inter-nucleosome interactions
title_short iNucs: inter-nucleosome interactions
title_sort inucs: inter-nucleosome interactions
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8652021/
https://www.ncbi.nlm.nih.gov/pubmed/34623394
http://dx.doi.org/10.1093/bioinformatics/btab698
work_keys_str_mv AT oveisimehrdad inucsinternucleosomeinteractions
AT shuklamanu inucsinternucleosomeinteractions
AT seymennogayhan inucsinternucleosomeinteractions
AT ohnomasae inucsinternucleosomeinteractions
AT taniguchiyuichi inucsinternucleosomeinteractions
AT nahatasunil inucsinternucleosomeinteractions
AT loosremco inucsinternucleosomeinteractions
AT muftighulamj inucsinternucleosomeinteractions
AT allshirerobinc inucsinternucleosomeinteractions
AT dimitrovstefan inucsinternucleosomeinteractions
AT karimimohammadm inucsinternucleosomeinteractions

Ejemplares similares