greenPipes: an integrated data analysis pipeline for greenCUT&RUN and CUT&RUN genome-localization datasets.
Bioinformatics
; 40(5)2024 May 02.
Article
en En
| MEDLINE
| ID: mdl-38718209
ABSTRACT
MOTIVATION To study gene regulation through transcription factors and chromatin modifiers, a variety of genome-wide techniques are used. Recently, CUT&RUN-based technologies have become popular, but a pipeline for the comprehensive analysis of CUT&RUN datasets is currently lacking. Here, we present the "greenPipes" package, which includes fine-tuned parameters specifically for bioinformatic analyses of greenCUT&RUN and CUT&RUN datasets. greenPipes provides additional functionalities for data analysis and data integration with other -omics technologies, which are either not available in other pipelines developed for CUT&RUN datasets or scattered in the literature as individual packages. AVAILABILITY AND IMPLEMENTATION Source code and a manual of the greenPipes are freely available on GitHub website (https//github.com/snizam001/greenPipes). The test datasets, comprehensive annotation files, and other datasets are available at https//osf.io/ruhj9/. CONTACT n.sheikh@dkfz-heidelberg.de or m.timmers@dkfz-heidelberg.de. SUPPLEMENTARY INFORMATION The handbook of greenPipes is available online at Bioinformatics as Supplementary text.
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Programas Informáticos
/
Biología Computacional
Límite:
Humans
Idioma:
En
Revista:
Bioinformatics
Asunto de la revista:
INFORMATICA MEDICA
Año:
2024
Tipo del documento:
Article
País de afiliación:
Alemania