chipchipnorm 1.0.1 – Normalize 2-color Microarray Data

chipchipnorm 1.0.1

:: DESCRIPTION

chipchipnorm (ChIP-chip normalization) is a R package that can be incorporated into the normalization workflow for chip-chip data, chromatin immunoprecipitation (ChIP) with microarray technology (chip).

:DEVELOPER

Peter Park’s lab at CBMI, Harvard Medical School

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux / MacOsX
R package

:: DOWNLOAD

chipchipnorm

:: MORE INFORMATION

Citation

Shouyong Peng, Artyom A Alekseyenko, Erica Larschan, Mitzi I Kuroda, and Peter J Park.
Normalization and experimental design for ChIP-chip data.
BMC Bioinformatics, 8(219), 2007.

ITALICS 2.52.0 – Normalize of Affymetrix GeneChip Human Mapping 100K and 500K set

ITALICS 2.52.0

:: DESCRIPTION

ITALICS (ITerative and Alternative normaLIzation and Copy number calling for affymetrix Snp arrays) is a normalization method that estimates both biological and non-relevant effects in an alternate, iterative manner, accurately eliminating irrelevant effects.

::DEVELOPER

U900 Institut Curie – INSERM/Mines ParisTech “Bioinformatics and Computational Systems Biology of Cancer

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ Windows/ MacOsX
R package
Bioconductor

:: DOWNLOAD

ITALICS

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Mar 15;24(6):768-74. doi: 10.1093/bioinformatics/btn048.
ITALICS: an algorithm for normalization and DNA copy number calling for Affymetrix SNP arrays.
Rigaill G, Hupé P, Almeida A, La Rosa P, Meyniel JP, Decraene C, Barillot E.

SQN 1.0 – Normalizes based a Subset of Negative Control Probes

SQN 1.0

:: DESCRIPTION

SQN (subset quantile normalization) normalizes based on the distribution of non-specific control features, without restriction on the behavior of specific signals.

::DEVELOPER

Zhijin Wu PhD

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
R package

:: DOWNLOAD

SQN

:: MORE INFORMATION

Citation

J Comput Biol. 2010 Oct;17(10):1385-95.
Subset quantile normalization using negative control features.
Wu Z, Aryee MJ.

tRMA 1.0 – Modification of RMA to Normalize Microarray Experiments

tRMA 1.0

:: DESCRIPTION

tRMA is a modification of RMA to normalize microarray experiments for correlation-based analysis.

::DEVELOPER

Usadel Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsX
R package

:: DOWNLOAD

tRMA

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Nov 11;11:553. doi: 10.1186/1471-2105-11-553.
Algorithm-driven artifacts in median Polish summarization of microarray data.
Giorgi FM, Bolger AM, Lohse M, Usadel B.

Moara 1.0.6 – Extract & Normalize Gene and Protein Mentions

Moara 1.0.6

:: DESCRIPTION

Moara is a software for gene mentions and normalization in biological texts.

::DEVELOPER

Moara team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsX
Java
MySQL
Weka
SecondString
ABNER

:: DOWNLOAD

Moara

:: MORE INFORMATION

Citation

Moara: a Java library for extracting and normalizing gene and protein mentions.
Neves ML, Carazo JM, Pascual-Montano A.
BMC Bioinformatics. 2010 Mar 26;11:157.

RZ-smooth 3.5 – Resample, Smooth and Normalize Microarray time-series data

RZ-smooth 3.5

:: DESCRIPTION

RZ-smooth is a tool to resample (upsample), smooth and to normalize the input microarray data. The results can be compromised without the data pre-processing. RZ-smooth program takes as an input a matrix, where rows correspond to individual genes and columns correspond to different time points.

::DEVELOPER

Dmitri Papatsenko

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows

:: DOWNLOAD

RZ-smooth

:: MORE INFORMATION

Citation

Goltsev Y, Papatsenko D.
“Time warping of evolutionary distant temporal gene expression data based on noise suppression”
BMC Bioinformatics. 2009 Oct 26;10:353.