Tag: Epigenomic data

GATE 20130701 – Genomic Annotation using Temporal Epigenomic data

GATE 20130701

:: DESCRIPTION

GATE is a probabilistic model to annotate the genome. This model detects similar but not neccesarily synchronous epigenomic changes in different genomic segments.

::DEVELOPER

Zhong Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 GATE

:: MORE INFORMATION

Citation

Yu PF, Xiao S, Xin XY, Song CX, Huang W, McDee D, Tanaka T, Wang T, He C, Zhong S. 2012.
Spatiotemporal clustering of epigenome reveals rules of dynamic gene regulation .
Genome Res. 2012 Dec 19.

EpiGRAPH 1.0 – Statistical Analysis and Prediction of Epigenomic data

EpiGRAPH 1.0

:: DESCRIPTION

EpiGRAPH enables biologists to analyze genome and epigenome datasets with powerful statistical and machine learning methods. In a typical workflow, the user uploads a set of genomic regions of interest (e.g. experimentally mapped enhancers, hotspots of epigenetic regulation or sites exhibiting disease-specific alterations), and EpiGRAPH searches a large database of (epi-) genomic attributes for significant overlap and correlation with the regions in the input dataset. Furthermore, EpiGRAPH can predict the status of genomic regions that were not included in the input dataset.

::DEVELOPER

Max-Planck-Institut Informatik

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 No

:: MORE INFORMATION

Citation

EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data.
Bock C, Halachev K, Büch J, Lengauer T.
Genome Biol. 2009 Feb 10;10(2):R14.

Epi-Speller – Analyze Multiple Genome-wide Profiling Epigenomic data

Epi-Speller

:: DESCRIPTION

Epi-Speller is a program for analyzing multiple genome-wide profiling epigenomic data.

::DEVELOPER

Huy Q. Dinh

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R package
  • C++ Compiler
  • Perl

:: DOWNLOAD

 Epi-Speller

:: MORE INFORMATION

Citation

Dinh HQ, Mittelsten Scheid O, von Haeseler A.
Epi-Speller – a bioinformatic tool for epigenomic signature discovery.
submitted.