Tag: Differential

diffReps 1.55.6 – Finding Differential Chromatin Modification Sites from ChIP-seq data

diffReps 1.55.6

:: DESCRIPTION

diffReps is developed to find different peaks in ChIP-seq. It scans the whole genome using a sliding window, performing millions of statistical tests and report the significant hits. diffReps takes into account the biological variations within a group of samples and uses that information to enhance the statistical power. Considering biological variation is of high importance, especiallly for in vivo brain tissues.

::DEVELOPER

SHEN LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

  diffReps

:: MORE INFORMATION

Citation

PLoS One. 2013 Jun 10;8(6):e65598. doi: 10.1371/journal.pone.0065598. Print 2013.
diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates.
Shen L, Shao NY, Liu X, Maze I, Feng J, Nestler EJ.

EDGE 2.22.0 – Extraction of Differential Gene Expression

EDGE 2.22.0

:: DESCRIPTION

EDGE is a software package for the significance analysis of DNA microarray experiments for both standard and time course experiments based on our new Optimal Discovery Procedure and Time Course Methodology

::DEVELOPER

Jeffrey Leek, Alan Dabney, Eva Monsen and John Storey.

:: SCREENSHOTS

EDGE

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • R
  • BioConductor

:: DOWNLOAD

EDGE

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Feb 15;27(4):509-15. doi: 10.1093/bioinformatics/btq701. Epub 2010 Dec 24.
A computationally efficient modular optimal discovery procedure.
Woo S, Leek JT, Storey JD.