DattaLab Software Page

All software/computer codes listed here are for non-commercial use only.

Furthermore, they are being distributed “as is” without any implicit or explicit

warrantee of any kind. In other words, use them at your own will and risk.

Bioinformatics Software

· R Code for SVPLS

References:

Chakraborty, S., Datta, S. and Datta, S. Surrogate variable analysis using partial least squares (SVA-PLS) in gene expression studies. Bioinformatics doi: 10.1093/bioinformatics/bts022 (2012).

· R Code for DNA (Differential Network Analysis)

References:

Gill, R., Datta, S. and Datta, S. A statistical framework for differential network analysis from microarray data using partial least squares, BMC Bioinformatics, 11, 95 (2010).

· R Code for Ensemble Classifier

References:

Datta, S, Pihur, V. and Datta, S. An adaptive optimal ensemble classifier via bagging and rank aggregation with applications to high dimensional data, BMC Bioinformatics, 11:427 (2010).

• R Package for Rank Aggregation

References:

Pihur, V., Datta, S. and Datta, S. RankAggreg, an R package for weighted rank aggregation. BMC Bioinformatics, 10, 62 (2009).

Pihur, V., Datta, S. and Datta, S. Weighted rank aggregation of cluster validation measures: A Monte Carlo cross-entropy approach. Bioinformatics, 23, 1607-1615 (2007).

• R Package for Cluster Validation

References:

Datta, S. and Datta, S. Methods for evaluating clustering algorithms for gene expression data using a reference set of functional classes, BMC Bioinformatics, 7:397 (2006).

Datta, S. and Datta, S. Comparisons and validation of statistical clustering techniques for microarray gene expression data. Bioinformatics, 19, 459-466 (2003).

• R code for Empirical Bayes Screening (EBS)

References:

Datta, S. and Datta, S. Empirical Bayes screening (EBS) of many p-values with applications to microarray studies, Bioinformatics, 21,1987-1994 (2005).

Proteomics Software

• Fortran code for Standardization and Denoising Mass Spectra

References:

Satten, G. A., Datta, S., Moura, H., Woolfitt, A., Carvalho, G., De, B. K, Pavlopoulos, A., Carlone, G. M., and Barr, J. Standardization and denoising algorithms for mass spectra to classify whole-organism bacterial specimens, Bioinformatics, 20, 3128-3136 (2004).

· Peak Detection and Classification using MALDI-TOF Mass Spectra

References:

Ndukum, J., Atlas, M., Datta, S. (2011). pkDACLASS: open source software for analyzing MALDI-TOF, Bioinformation, 6, 45-47. PMC3064853

Statistics Software

• R-codes for Rank Sum Test for Clustered Data 2 groups m groups

References:

Datta, S. and Satten, G. A. Rank-sum tests for clustered data, Journal of the American Statistical Association, 100, 908-915 (2005).

• R-codes for Signed Rank Test for Clustered Data

References:

Datta, S. and Satten, G. A. A signed-rank test for clustered data, Biometrics, 64, 501-507 (2008).

• R-codes for Marginal Association Measures for Clustered Data

References:

Lorenz, D. J., Datta, S. and Harkema, S. J. Marginal association measures for clustered data, Statistics in Medicine, 30, 3181-3191 (2011).