Sole-Search v2 – Peak Detection and Functional Annotation using ChIP-seq data

Sole-Search v2

:: DESCRIPTION

Sole-Search is an integrated peak-calling and analysis softwar which is available through a user-friendly interface and (i) converts raw data into a format for visualization on a genome browser, (ii) outputs ranked peak locations using a statistically based method that overcomes the significant problem of false positives, (iii) identifies the gene nearest to each peak, (iv) classifies the location of each peak relative to gene structure, (v) provides information such as the number of binding sites per chromosome and per gene and (vi) allows the user to determine overlap between two different experiments.

::DEVELOPER

Korf Lab at the University of California, Davis.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Perl

:: DOWNLOAD

 Sole-Search

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2010 Jan;38(3):e13. doi: 10.1093/nar/gkp1012. Epub 2009 Nov 11.
Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data.
Blahnik KR, Dou L, O’Geen H, McPhillips T, Xu X, Cao AR, Iyengar S, Nicolet CM, Lud?scher B, Korf I, Farnham PJ.

TileMap v2 – Tiling Array Peak Detection

TileMap v2

:: DESCRIPTION

TileMap is a tool designed for tiling array data analysis. It can be used to identify genomic loci that show transcriptional activities and transcription factor binding patterns of interest.

::DEVELOPER

Ji Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Unix

:: DOWNLOAD

TileMap

:: MORE INFORMATION

Citation

Ji, H. and Wong, W.H. (2005)
TileMap: create chromosomal map of tiling array hybridizations.
Bioinformatics, 21(18):3629-3636.

peakrots 1.01 – Optimized procedure for ChIP-seq Peak Detection

peakrots 1.01

:: DESCRIPTION

peakrots is a bioinformatics analysis tool for optimized ChIP-seq peak detection.

::DEVELOPER

Laura Elo  , Aleksi Kallio  at CSC — IT Center for Science Ltd

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • R package

:: DOWNLOAD

 peakrots

:: MORE INFORMATION

Citation

Methods Mol Biol. 2013;1038:181-91. doi: 10.1007/978-1-62703-514-9_11.
Optimizing Detection of Transcription Factor-Binding Sites in ChIP-seq Experiments.
Kallio A, Elo LL.