Tag: RSEG

RSEG 0.4.9 – Identify Epigenomic Domains from ChIP-Seq data

RSEG 0.4.9

:: DESCRIPTION

The RSEG software package is aimed to analyze ChIP-Seq data, especially for identifying genomic regions and their boundaries marked by diffusive histone modification markers, such as H3K36me3 and H3K27me3. It can work with or without control sample. It can be used to find regions with differential histone modifications patterns, either comparsion between two cell types or between two kinds of histone modifications.

::DEVELOPER

The Smith Lab

:: SCREENSHOTS

Command

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RSEG

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Mar 15;27(6):870-1. Epub 2011 Feb 16.
Identifying dispersed epigenomic domains from ChIP-Seq data.
Song Q, Smith AD.

Rseg 1.0 – an R package to Optimize Segmentation of SNP array data

Rseg 1.0

:: DESCRIPTION

Rseg allows the user to define sample-specific thresholds to call gains and losses in an interactive way. It also allows the user to correct for RMA induced normalization artifacts in case of imbalance between losses and gains.

::DEVELOPER

Lamy P (plamy@cs.au.dk), Wiuf C, Ørntoft TF, Andersen CL.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • R package

:: DOWNLOAD

 Rseg

:: MORE INFORMATION

Citation

Rseg–an R package to optimize segmentation of SNP array data.
Lamy P, Wiuf C, Ørntoft TF, Andersen CL.
Bioinformatics. 2011 Feb 1;27(3):419-20.