DANPOS pipeline

DANPOS specifications

Information


Unique identifier OMICS_00502
Name DANPOS
Alternative name Dynamic Analysis of Nucleosome and Protein Occupancy by Sequencing
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python, R
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.2.2
Stability Stable
Requirements Req: rpy, numpy, Samtools
Maintained Yes

Download


Versioning


Add your version

Documentation


Maintainer


  • person_outline Wei Li <>

Publication for Dynamic Analysis of Nucleosome and Protein Occupancy by Sequencing

DANPOS IN pipeline

2017
PMCID: 5487215
PMID: 28653622
DOI: 10.7554/eLife.23203.062

[…] of these datasets were lifted from hg19 to hg38 using liftover (kent et al., 2002) (default re-mapping ratio 0.95). nucleosome positions based on mnase-seq data in gm12878 were determined with danpos version 2.2.2 (chen et al., 2013) using default settings. resulting intervals were lifted to hg38. after removing summit locations with occupancy values above 300, the top 5% (713361) […]

DANPOS institution(s)
Division of Biostatistics, Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA; Department of Genetics and Institute of Diabetes, Obesity, and Metabolism, School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Center for Cancer Epigenetics, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA; Department of Biochemistry and Molecular Biology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA; Department of Molecular Carcinogenesis, Science Park, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
DANPOS funding source(s)
Supported in part by Cancer Prevention and Research Institute of Texas grant RP110471-C3, DOD grant PC094421, and 973 project 2010CB944900 of China and NIH grant HG004840.

DANPOS review

star_border star_border star_border star_border star_border
star star star star star

avilella

star_border star_border star_border star_border star_border
star star star star star
Desktop
Easy to download and run. Minimal dependencies.