Mixer 1.03 – ChIP-chip Analysis by Mixture Model approach

Mixer 1.03

:: DESCRIPTION

Mixer is a mixture model approach to analyze ChIP-chip or ChIP-seq data, also with some utility functions to process DNA sequence data. It includes statistical methods for both data normalization and peak detection. The peak detection and quantification relies on a mixer model approach that dissects the distribution of background signals and the Immunoprecipitated signals. In contrast to many existing methods, mixer is more flexible by imposing less restrictive assumptions and allowing a relatively large proportion of peak regions. Robust performance on data sets predicted to contain numerous peaks is very important for the studies of the transcription factors with abundant binding sites, and common chromatin features or epigenetic marks.

::DEVELOPER

Wei Sun

:: SCREENSHOTS

N/A

::REQUIREMENTS

:: DOWNLOAD

  Mixer

:: MORE INFORMATION

Citation

Wei Sun, Michael J Buck, Mukund Patel and Ian J Davis (2009),
Improved ChIP-chip analysis by mixture model approach.
BMC Bioinformatics 2009, 10:173

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.

ChIPper – Analysis of ChIP-chip data

ChIPper

:: DESCRIPTION

Chipper is a software of discovering transcription-factor targets from chromatin immunoprecipitation microarrays using variance stabilization.

::DEVELOPER

Roth Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ChIPper

:: MORE INFORMATION

Citation

Genome Biol. 2005;6(11):R96. Epub 2005 Nov 1.
Chipper: discovering transcription-factor targets from chromatin immunoprecipitation microarrays using variance stabilization.
Gibbons FD, Proft M, Struhl K, Roth FP.

W-ChIPeaks – Process ChIP-chip and ChIP-seq data

W-ChIPeaks

:: DESCRIPTION

W-ChIPeaks employs a probe-based or bin-based enrichment threshold to define peaks and applies statistical methods to control the false discovery rate for identified peaks.

::DEVELOPER

Jin Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Feb 1;27(3):428-30. doi: 10.1093/bioinformatics/btq669. Epub 2010 Dec 7.
W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data.
Lan X, Bonneville R, Apostolos J, Wu W, Jin VX.

MeDiChI 0.4.1 – Model-Based ChIP-chip Deconvolution Algorithm

MeDiChI 0.4.1

:: DESCRIPTION

MeDiChI is method for the automated, model-based deconvolution of protein-DNA binding (Chromatin immunoprecipitation followed by hybridization to a genomic tiling microarray — ChIP-chip) data that discovers DNA binding sites at high resolution (higher resolution than that of the tiling array itself).

::DEVELOPER

Baliga Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package

:: DOWNLOAD

 MeDiChI

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Feb 1;24(3):396-403. Epub 2007 Dec 1.
Model-based deconvolution of genome-wide DNA binding.
Reiss DJ, Facciotti MT, Baliga NS.

Ringo 1.57.0 – Analysis of ChIP-chip data

Ringo 1.57.0

:: DESCRIPTION

Ringo is an R package that facilitates the analysis of ChIP-chip experiments by providing functionality for data import, quality assessment, normalization and visualization of the data, and the detection of ChIP-enriched genomic regions.

::DEVELOPER

Huber Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

   Ringo

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2007 Jun 26;8:221.
Ringo–an R/Bioconductor package for analyzing ChIP-chip readouts.
Toedling J, Skylar O, Krueger T, Fischer JJ, Sperling S, Huber W.

Starr 1.38.0 – Simple Tiling ARRay analysis of Affymetrix ChIP-chip data

Starr 1.38.0

:: DESCRIPTION

Starr is open-source R/Bioconductor package that facilitates comparative analysis of ChIP-chip data across experiments and across different microarray platforms.

::DEVELOPER

Starr  team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 Starr

:: MORE INFORMATION

Citation

Starr: Simple Tiling ARRay analysis of Affymetrix ChIP-chip data.
Zacher B, Kuan PF, Tresch A.
BMC Bioinformatics. 2010 Apr 17;11:194. doi: 10.1186/1471-2105-11-194.

JAMIE 0.91 – Joint Analysis of Multiple ChIP-chip Experiments

JAMIE 0.91

:: DESCRIPTION

JAMIE (Joint Analysis of Multiple IP Experiments) is a R package to perform the joint analysis. The genome is assumed to consist of background and potential binding regions (PBRs). PBRs have context-dependent probabilities to become bona fide binding sites in individual datasets. This model captures the correlation among datasets, which provides basis for sharing information across experiments. Real data tests illustrate the advantage of JAMIE over a strategy that analyzes individual datasets separately.

::DEVELOPER

Ji Lab
:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

JAMIE

:: MORE INFORMATION

Citation

Wu H. and Ji H. (2010)
JAMIE: Joint analysis of multiple ChIP-chip experiments.
Bioinformatics (2010) 26 (15): 1864-1870.

CisGenome 2.0 – ChIP-chip and ChIP-seq Data Analysis

CisGenome 2.0

:: DESCRIPTION

CisGenome is a software system for analyzing genome-wide chromatin immunoprecipitation (ChIP) data. CisGenome is designed to meet all basic needs of ChIP data analyses, including visualization, data normalization, peak detection, false discovery rate computation, gene-peak association, and sequence and motif analysis. In addition to implementing previously published ChIP–microarray (ChIP-chip) analysis methods, the software contains statistical methods designed specifically for ChlP sequencing (ChIP-seq) data obtained by coupling ChIP with massively parallel sequencing. The modular design of CisGenome enables it to support interactive analyses through a graphic user interface as well as customized batch-mode computation for advanced data mining. A built-in browser allows visualization of array images, signals, gene structure, conservation, and DNA sequence and motif information.

::DEVELOPER

Ji Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX /  Linux

:: DOWNLOAD

CisGenome

:: MORE INFORMATION

Citation

Hongkai Ji, Hui Jiang, Wenxiu Ma, David S. Johnson, Richard M. Myers and Wing H.Wong (2008)
An integrated software system for analyzing ChIP-chip and ChIP-seq data.
Nature Biotechnology, 26: 1293-1300. doi:10.1038/nbt.1505

ChIPpeakAnno 3.24.2 – Annotate ChIP-seq and ChIP-chip data

ChIPpeakAnno 3.24.21

:: DESCRIPTION

ChIPpeakAnno is a Bioconductor package within the statistical programming environment R to facilitate batch annotation of enriched peaks identified from ChIP-seq, ChIP-chip, cap analysis of gene expression (CAGE) or any experiments resulting in a large number of enriched genomic regions.

::DEVELOPER

Program in Gene Function and Expression@umassmed

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • BioConductor
  • R package

:: DOWNLOAD

  ChIPpeakAnno

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2010 May 11;11:237. doi: 10.1186/1471-2105-11-237.
ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data.
Zhu LJ, Gazin C, Lawson ND, Pagès H, Lin SM, Lapointe DS, Green MR.

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