MAT build 3 – Model-based Analysis of Tiling-arrays for ChIP-chip

MAT build 3

:: DESCRIPTION

MAT (Model-based Analysis of Tiling-array) detect regions enriched by transcription factor chromatin immunoprecipitation (ChIP) on Affymetrix tiling arrays (ChIP-chip). MAT models the baseline probe behavior by considering probe sequence and copy number on each array. It standardizes the probe value through the probe model, eliminating the need for sample normalization. MAT uses an innovative function to score regions for ChIP enrichment, which allows robust P value and false discovery rate calculations. MAT can detect ChIP regions from a single ChIP sample, multiple ChIP samples, or multiple ChIP samples with controls with increasing accuracy. The single-array ChIP region detection feature minimizes the time and monetary costs for laboratories newly adopting ChIP-chip to test their protocols and antibodies and allows established ChIP-chip laboratories to identify samples with questionable quality that might contaminate their data.

::DEVELOPER

X. Shirley Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MAT

:: MORE INFORMATION

Citation:

Johnson WE, Li W, Meyer CA, Gottardo R, Carroll JS, Brown M and Liu XS:
Model-based analysis of tiling-arrays for ChIP-chip.
Proc. Natl. Acad. Sci. USA 103 (2006) 12457-12462.

tilingArray 1.47.0 – Transcript mapping with high-density oligonucleotide tiling arrays

tilingArray 1.47.0

:: DESCRIPTION

tilingArray provides functionality that can be useful for the analysis of high-density tiling microarray data (such as from Affymetrix genechips) for measuring transcript abundance and architecture.

::DEVELOPER

Huber Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

  tilingArray

:: MORE INFORMATION

Citation

Bioinformatics. 2006 Aug 15;22(16):1963-70. Epub 2006 Jun 20.
Transcript mapping with high-density oligonucleotide tiling arrays.
Huber W, Toedling J, Steinmetz LM.

CMARRT 1.3 – Analysis of ChIP-Chip data from Tiling Arrays

CMARRT 1.3

:: DESCRIPTION

CMARRT (Correlation, Moving Average, Robust and Rapid method on Tiling array) is an R package for the analysis of tiling array data that incorporates the correlation structures among probe measurements.

::DEVELOPER

Pei Fen Kuan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 CMARRT

:: MORE INFORMATION

Citation

Kuan, P., Chun, H., and Keles, S. (2008).
CMARRT: A tool for the analysis of ChIP-Chip data from tiling arrays by incorporating the correlation structure.
Pac Symposium of Biocomputing, 515-526.

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

Hongkai Ji’s Research Group , The Johns Hopkins University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Unix

:: DOWNLOAD

TileMap for Win , For Unix

:: MORE INFORMATION

Citation

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

TileShuffle 0.2.0 – Statistical Analysis of Tiling Array Expression Data

TileShuffle 0.2.0

:: DESCRIPTION

TileShuffle is a software of detection of transcribed or differentially expressed segments in tiling array data by permutation testing.This package contains functions for the analysis of tiling array data. It implements a statistical approach to detect expression or differential expression in terms of differences from the background distribution that avoids any intensity-related parameters. Moreover, it reduces the most dominant tiling array biases using an affinity-dependent permutation in conjunction with a windowing approach.

::DEVELOPER

Kristin Reiche

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 TileShuffle

:: MORE INFORMATION