CNVineta 1.0-1 – Data mining tool for large case-control copy number variation data sets

CNVineta 1.0-1

:: DESCRIPTION

CNVineta is a flexible data mining tool for the analysis of copy number variations (CNVs) in large case-control SNP array data sets. The tool is available as an R statistical package. CNVineta offers a flexible and fast access to CNVs by a quick graphical overview in large case-control datasets. In addition, CNVineta provides rapid access to the log2 of raw data ratios (LRR) and B-allele frequencies (BAF) of specific or all samples, thereby allowing for a fast verification of the underlying raw data. CNVineta is also equipped with analysis methods for genome-wide screening for associated rare as well as common CNVs. Hence, CNVineta is a unique data mining tool to rapidly explore CNVs in large case-control data sets.

::DEVELOPER

Institute for Clinical Molecular Biology

:: SCREENSHOTS

N/A

::REQUIREMENTS

:: DOWNLOAD

 CNVineta

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Sep 1;26(17):2208-9. Epub 2010 Jul 6.
CNVineta: a data mining tool for large case-control copy number variation datasets.
Wittig M, Helbig I, Schreiber S, Franke A.

SPICE 6.1001 – Data Mining & Visualization Software for Multicolor Flow Cytometry

SPICE 6.1001

:: DESCRIPTION

SPICE is a data mining software application that analyzes large FLOWJO data sets from polychromatic flow cytometry and organizes the normalized data graphically. SPICE enables users to discover potential correlations in their experimental data within complex data sets.

::DEVELOPER

Bioinformatics and Computational Biosciences Branch (BCBB),National Institute of Allergy and Infectious Diseases (NIAID)

:: SCREENSHOTS

SPICE

:: REQUIREMENTS

  • Mac OsX

:: DOWNLOAD

 SPICE

:: MORE INFORMATION

Citation

Cytometry A. 2011 Feb;79(2):167-74. doi: 10.1002/cyto.a.21015. Epub 2011 Jan 7.
SPICE: exploration and analysis of post-cytometric complex multivariate datasets.
Roederer M, Nozzi JL, Nason MC.

IntOGen 2020-02-01 – Integration and Data Mining of multidimensional Oncogenomic data

IntOGen 2020-02-01

:: DESCRIPTION

IntOGen (Integrative OncoGenomics), a discovery tool for cancer researchers, is a resource that integrates multidimensional OncoGenomics Data for the identification of genes and groups of genes (biological modules) involved in cancer development.

::DEVELOPER

 The Biomedical Genomics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 No

:: MORE INFORMATION

Citation

IntOGen: integration and data mining of multidimensional oncogenomic data.
Gundem G, Perez-Llamas C, Jene-Sanz A, Kedzierska A, Islam A, Deu-Pons J, Furney SJ, Lopez-Bigas N.
Nat Methods. 2010 Feb;7(2):92-3

Strand NGS v4.0 – Data Mining and Visualization Platform of Bioinformatics Data

Strand NGS v4.0

:: DESCRIPTION

Strand NGS (Formerly Avadis NGS) is an integrated platform that provides analysis, management and visualization tools for next-generation sequencing data. It supports extensive workflows for alignment, RNA-Seq, small RNA-Seq, DNA-Seq, Methyl-Seq, MeDIP-Seq, and ChIP-Seq experiments.

::DEVELOPER

Strand Scientific Intelligence, Inc.

:: SCREENSHOTS

AvadisNGS

:: REQUIREMENTS

  • Windows/MacOsX/Linux

:: DOWNLOAD

Strand NGS

:: MORE INFORMATION

PolyFARM 0.3.4 – Data Mining software for Relational Data

PolyFARM 0.3.4

:: DESCRIPTION

PolyFARM (Poly-machine First-order Association Rule Mining) is a data mining program which finds first order associations in Datalog data.

::DEVELOPER

PolyFARM team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PolyFARM

:: MORE INFORMATION

Citation

Bioinformatics. 2003 Oct;19 Suppl 2:ii42-9.
Predicting gene function in Saccharomyces cerevisiae.
Clare A, King RD.

Manteia v.7.0 – Data Mining system for Vertebrate Genes

Manteia v.7.0

:: DESCRIPTION

Manteia is an advanced data mining system that allows researchers to combine a variety of data and tools in order to test hypotheses and address complex biological questions.

::DEVELOPER

Manteia team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Manteia, a predictive data mining system for vertebrate genes and its applications to human genetic diseases.
Tassy O, Pourquié O.
Nucleic Acids Res. 2014 Jan 1;42(1):D882-91. doi: 10.1093/nar/gkt807.

Orange-Bioinformatics 3.28.0 – Orange Bioinformatics add-on for Orange data mining software package

Orange-Bioinformatics 3.28.0

:: DESCRIPTION

Orange Bioinformatics is an add-on for Orange data mining software package. It extends Orange by providing common functionality for basic tasks in bioinformatics. It also provides widgets for Orange Canvas, which enable users who are not programmers to manage microarray and genomic data flow and to customize their analysis by combining common data analysis tools to fit their needs.

::DEVELOPER

BioLab , University of Ljubljana

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 Orange-Bioinformatics

:: MORE INFORMATION

Citation:

Tomaž Curk, Janez Demšar, Qikai Xu, Gregor Leban, Uroš Petrovič, Ivan Bratko, Gad Shaulsky, Blaž Zupan.
Microarray data mining with visual programming.
Bioinformatics. 2005 Feb 1;21(3):396-8.

PICA – Genotype-phenotype data Mining software

PICA

:: DESCRIPTION

PICA (Phenotype Investigation with Classification Algorithms) is a Python framework for testing genotype-phenotype association algorithms.

::DEVELOPER

CUBE – Bioinformatics and Computational Systems Biology, University of Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PICA

:: MORE INFORMATION

Citation:

Bioinformatics. 2010 Aug 1;26(15):1834-40. Epub 2010 Jun 6.
Efficient learning of microbial genotype-phenotype association rules.
MacDonald NJ, Beiko RG.

Weka-CG 0.1.1 – Data Mining software package for Human Genetics

Weka-CG 0.1.1

:: DESCRIPTION

Weka-CG is a comprehensive data mining software package for human genetics. It is an extension of the open-source, JAVA-based, Weka data mining package.

::DEVELOPER

the Computational Genetics Laboratory in the Institute for Quantitative Biomedical Sciences at Dartmouth Medical Schooland Dartmouth College

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Weka-CG

:: MORE INFORMATION

HapMiner 1.1 – Haplotype-based Linkage Disequilibrium mapping via direct Data Mining

HapMiner 1.1

:: DESCRIPTION

HapMiner is a computer program for association mapping based on directly mining the haplotypes from case-control data via a density-based clustering algorithm. HapMiner can be applied to whole-genome screens, as well as candidate-gene studies in small genomic regions.

::DEVELOPER

Jing Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

 HapMiner

:: MORE INFORMATION

Citation

Li and Jiang (2005),
Haplotype-based linkage disequilibrium mapping via direct data mining
Bioinformatics, 21(24):4384-4393.