DANPOS 2.2.2 – Dynamic Analysis of Nucleosome Position and Occupancy by Sequencing

DANPOS 2.2.2

:: DESCRIPTION

DANPOS is designed for genome-wide comparative analysis of nucleosome maps. It detect single-nucleotide-resolution change in positions(location), enrichment (occupancy), and fuzziness (phasing, positioning) of each nucleosome unit.

::DEVELOPER

Wei Li’s Computational Epigenomics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python
R package
Samtool

:: DOWNLOAD

DANPOS

:: MORE INFORMATION

Citation:

Genome Res. 2013 Feb;23(2):341-51. doi: 10.1101/gr.142067.112. Epub 2012 Nov 28.
DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing.
Chen K, Xi Y, Pan X, Li Z, Kaestner K, Tyler J, Dent S, He X, Li W.

idFBA – Dynamic analysis of integrated Signaling, Metabolic, and Regulatory Networks

idFBA

:: DESCRIPTION

idFBA (integrated dynamic FBA) is a flux balance analysis (FBA)-based strategy that dynamically simulates cellular phenotypes arising from integrated networks.

::DEVELOPER

the Computational Systems Biology Laboratory, Department of Biomedical Engineering, University of Virginia.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX
MatLab

:: DOWNLOAD

idFBA

:: MORE INFORMATION

Citation:

Lee, J.M., E.P. Gianchandani, J.A. Eddy, and J.A. Papin. 2008.
Dynamic analysis of integrated signaling, metabolic, and regulatory networks.
PLoS Computational Biology, 4(5): e1000086

DaPars 0.9.1 – Dynamic analysis of Alternative PolyAdenylation from RNA-seq

DaPars 0.9.1

:: DESCRIPTION

DaPars is a novel bioinformatics algorithm for the de novo identification of dynamic APAs from standard RNA-seq.

::DEVELOPER

Li Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

DaPars

:: MORE INFORMATION

Citation:

Xia, Z., Donehower, L.A., Wheeler, D.A., Cooper, T.A., Neilson, J.R., Wagner E.J., Li, W. 2014.
Dynamic Analyses of Alternative Polyadenylation from RNA-Seq Reveal 3′-UTR Landscape Across 7 Tumor Types.
Nature Communications, 5:5274.