Bmc Bioinformatics Journal

Performs Mantel-Haenszel's test for k strata of 2x2 tables.Mantel and Haenszel proposed this asymptotic test based on the chi-2 distribution. Assuming no three-way interaction (k independent strata). Ref.: DeltaProt toolbox at http://services.cbu.uib.no/software/deltaprot/Input: X: data matrix...

Chi-square tests of homogeneity and independence.Computes the P-value for I x J - table row/col independence.Ref.: DeltaProt toolbox at http://services.cbu.uib.no/software/deltaprot/Input:X: data matrix (I x J -table) of the observed frequency cells.method: 'RC': Read-Cressie power divergence...

It is a non-parametric statistical test for discrete data used todetermine if there are nonrandom associations between the two variables.Mid-P values are a reasonable compromise between the conservativeness ofthe ordinary exact test and the uncertain adequacy of large-sample methods.Mid-P values...


Platforms: Matlab

AutoSOME is a new unsupervised multidimensional clustering method for identifying clusters of diverse shapes and sizes from large numerical datasets without prior knowledge of cluster number (BMC Bioinformatics, 11:117). Given the general nature of data clustering, AutoSOME has utility for a wide...


Platforms: Mac

The package generates a feature table from a batch of LC/MS spectra in .cdf format. Instructions: http://www.sph.emory.edu/apLCMS/ References Bioinformatics. 25(15):1930-36. BMC Bioinformatics. 11:559.


Platforms: Windows, Mac, BSD

CNV Workshop is a web-enabled platform for analyzing genome variation such as copy number variation (CNV). Learn about CNV Workshop in our associated BMC Bioinformatics manuscript: http://www.biomedcentral.com/1471-2105/11/74


Platforms: Windows, Mac, BSD, Linux

An R package that performs forward-backward fragment assembling segmentation. Reference: BMC Bioinformatics. 2007 May 3;8:145.


Platforms: Windows, Mac, Linux

This is the high throughput PCR primer design software that is used at the J. Craig Venter Institute. See: Li K, et al. 'Novel computational methods for increasing PCR primer design effectiveness in directed sequencing'. BMC Bioinformatics 2008, 9:191.


Platforms: Windows, Mac, Linux

PheMaDB is a web-based data management system to store and analyze OmniLog Phenotype Microarray data. The manuscript can be accessed here: http://www.biomedcentral.com/1471-2105/12/109. Chang WE et al. BMC Bioinformatics. 2011 Apr 20;12(1):109.


Platforms: Mac

A cumulative Mann-Kendall trend test.Calculating p-values for monotonic trend of ordinal data sequences(e.g. proteins) by a compound test based on Kendall's rank correlation.Ref.: The DeltaProt toolbox at http://services.cbu.uib.no/software/deltaprot/Use: pval = cumKendallTest(Q,pop,tail)returns...


Platforms: Matlab

COMPUTEGTOM computes the generalized overlaping measure algorithm (GTOM) [1]AuthorsJoaquin GodoT-i &IdoT-igo Martincorena University of Navarra -Dpt. of Physics and Applied Mathematics &Centre for Applied Medical Research. Pamplona (Spain). November 22nd, 2007batchComputeGTOM.m contains an...


Platforms: Matlab

ErmineJ performs analyses of gene sets in expression microarray data or other genome-wide data that results in rankings of genes. A typical goal is to determine whether particular biological pathways are "doing something interesting" in the data. The software is designed to be used by biologists...


Platforms: Mac

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Platforms: Windows

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Platforms: Windows

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Platforms: Windows

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Platforms: Windows, Windows CE

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Platforms: Windows

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Platforms: *nix

VLinux Bioinformatics workbench is a Linux distribution for Bioinformatics. It is easy to use, no installation required, CD-based distribution based on Knoppix 3.3. VLinux Bioinformatics Workbench includes a variety of sequence and structure analysis packages. It is an Open source product...


Platforms: *nix

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Platforms: Windows, Windows 8, Windows 7, Windows Server