Category: Microarray Analysis

iCall – Genotype-calling algorithm for rare and common Variants on the Illumina Exome Array.

iCall

:: DESCRIPTION

iCall is an improved genotype-calling algorithm for rare and common variants on the Illumina exome array. The algorithm does not rely on having prior training data and it can asssign genotypes to hybridization data from thousands of individuals simultaneously.

::DEVELOPER

Saw Swee Hock School of Public Health

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • C++ Compiler

:: DOWNLOAD

 iCall

 :: MORE INFORMATION

Citation

iCall: a genotype-calling algorithm for rare, low-frequency and common variants on the Illumina exome array.
Zhou J, Tantoso E, Wong LP, Ong RT, Bei JX, Li Y, Liu J, Khor CC, Teo YY.
Bioinformatics. 2014 Mar 12.

E-Predict 1.0 – Microarray-based Species Identification

E-Predict 1.0

:: DESCRIPTION

E-Predict compares observed hybridization patterns with theoretical energy profiles representing different species. We demonstrate the application of the algorithm to viral detection in a set of clinical samples and discuss its relevance to other metagenomic applications.

::DEVELOPER

DeRisi Lab, UCSF

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Apache
  • Perl

:: DOWNLOAD

 E-Predict

:: MORE INFORMATION

Citation

Urisman A, Fischer KF, Chiu CY, Kistler AL, Beck S, Wang D, DeRisi JL.
E-Predict: A Computational Strategy for Species Identification Based on Observed DNA Microarray Hybridization Patterns.
Genome Biology 2005, 6:R78

 

TIPMaP – Transcript Isoform Profiles from Microarray Probes

TIPMaP

:: DESCRIPTION

TIPMaP is a tool developed to identify differentially regulated transcripts (specific to human, mouse and rat).

::DEVELOPER

Institute of Bioinformatics and Applied Biotechnology, Bangalore, India,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Chitturi N, Balagannavar G, Chandrashekar DS, Abinaya S, Srini VS, Acharya KK.
TIPMaP: a web server to establish transcript isoform profiles from reliable microarray probes.
BMC Genomics. 2013 Dec 27;14:922. doi: 10.1186/1471-2164-14-922. PMID: 24373374; PMCID: PMC3884118.

MOSAICS 1.0.0 – Analysis of ChIP-seq data

MOSAICS 1.0.0

:: DESCRIPTION

MOSAICS is an R package for the analysis of one-sample or two-sample ChIP-seq data.

::DEVELOPER

Pei Fen Kuan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MOSAICS

:: MORE INFORMATION

Citation

Kuan, P., Chung, D., Pan, G., Thomson, J., Stewart, R., and Keles, S. (2011).
A Statistical Framework for the Analysis of ChIP-Seq Data.
Journal of the American Statistical Association

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.

GeneSelector 1.0 – Find Small subset of Genes for Classification of Expression data

GeneSelector 1.0

:: DESCRIPTION

GeneSelector finds a small subset of genes for classification of expression data.

::DEVELOPER

Ari Frank. @Laboratory of Computational Biology , Technion

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 GeneSelector

:: MORE INFORMATION

smoothseg 0.0.4 – Robust smooth segmentation approach for array CGH data analysis

smoothseg 0.0.4

:: DESCRIPTION

smoothseg is an R package to compute smooth-segmentation of array CGH data, including the estimation of FDR for comparative studies.

::DEVELOPER

Huang Jian <j.huang@ucc.ie>,  Prof. Yudi Pawitan ,Arief Gusnanto <Arief.Gusnanto@mrc-bsu.cam.ac.uk>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux /MacOsX
  • R package

:: DOWNLOAD

 smoothseg

:: MORE INFORMATION

Citation

Bioinformatics. 2007 Sep 15;23(18):2463-9. Epub 2007 Jul 27.
Robust smooth segmentation approach for array CGH data analysis.
Huang J1, Gusnanto A, O’Sullivan K, Staaf J, Borg A, Pawitan Y.

FLUSH.LVS 1.3.2 – Compute LVS Normalization and FLUSH filtering

FLUSH.LVS 1.3.2

:: DESCRIPTION

FLUSH.LVS is an R package to compute LVS (least-variant set) normalization and FLUSH (Filtering Likely Uninformative Sets of Hybridizations) filtering

::DEVELOPER

Prof. Yudi Pawitan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux /MacOsX
  • R package

:: DOWNLOAD

 FLUSH.LVS

 :: MORE INFORMATION

Citation

BMC Bioinformatics. 2008 Mar 5;9:140. doi: 10.1186/1471-2105-9-140.
Normalization of oligonucleotide arrays based on the least-variant set of genes.
Calza S1, Valentini D, Pawitan Y.

Nucleic Acids Res. 2007;35(16):e102. Epub 2007 Aug 15.
Filtering genes to improve sensitivity in oligonucleotide microarray data analysis.
Calza S1, Raffelsberger W, Ploner A, Sahel J, Leveillard T, Pawitan Y.

opm 1.1.0 – Analysing Phenotype Microarray and Growth Curve Data

opm 1.1.0

:: DESCRIPTION

opm is an R package designed to analyse multidimensional OmniLog phenotype microarray (PM) data.

::DEVELOPER

Leibniz Institute DSMZ

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package

:: DOWNLOAD

 opm

 :: MORE INFORMATION

Citation

Bioinformatics. 2013 Jul 15;29(14):1823-4. doi: 10.1093/bioinformatics/btt291. Epub 2013 Jun 5.
opm: an R package for analysing OmniLog(R) phenotype microarray data.
Vaas LA1, Sikorski J, Hofner B, Fiebig A, Buddruhs N, Klenk HP, Goker M.

LIMMA 3.50.0 – Linear Models for Microarray Data

LIMMA 3.50.0

:: DESCRIPTION

LIMMA is a software package for the analysis of gene expression microarray data, especially the use of linear models for analysing designed experiments and the assessment of differential expression. The package includes pre-processing capabilities for two-colour spotted arrays. The differential expression methods apply to all array platforms and treat Affymetrix, single channel and two channel experiments in a unified way.

::DEVELOPER

WEHI Bioinformatics

:: REQUIREMENTS

:: DOWNLOAD

 LIMMA

:: MORE INFORMATION

Citation

Smyth, G. K. (2005).
Limma: linear models for microarray data.
Bioinformatics and Computational Biology Solutions using R and Bioconductor, R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (eds.),
Springer, New York, pages 397-420

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