R Packages

HWELOH

Category: Genomics
Website: http://mendel.gene.cwru.edu/laframboiselab/software.php
PI: Thomas LaFramboise

Hardy-Weinberg Disequilibrium based method of calling LOH

RankCopy

Category: Genomics/Systems Biology
Website:http://mendel.gene.cwru.edu/laframboiselab/software.php
PI: Thomas LaFramboise
Reference: LaFramboise et al., Bioinformatics 2009

Nonparametric Methods to Detect Copy Number Variation, Containing rank-based methods to detect copy number change from raw array data

PLASQ

Category: Genomics/Systems Biology
Website: http://mendel.gene.cwru.edu/laframboiselab/software.php
PI: Thomas LaFramboise

Probe-Level Allele-specific Quantitation, containing methods to find allele- and parent-specific copy numbers from 100K SNP array data

MVR

Category: Bioinformatics/Statistics
Website: http://cran.r-project.org/web/packages/MVR/index.html
PI: Jean-Eudes Dazard
Reference: Dazard J-E., Rao J.S. Joint Adaptive Mean-Variance Regularization and Variance Stabilization of High Dimensional Data. Computational Statistics and Data Analysis (2012) 56(7) 2317-2333.

MVR is a non-parametric method for joint adaptive mean-variance regularization and variance stabilization of high-dimensional data. It is suited for handling difficult problems posed by high-dimensional multivariate datasets (p >> n paradigm), such as in omics-type data, among which are that the variance is often a function of the mean, variable-specific estimators of variances are not reliable, and tests statistics have low powers due to a lack of degrees of freedom.

ROCS

Category:Proteomics/Interactomics
Website:http://cran.r-project.org/web/packages/ROCS/index.html (to appear)
PI: Jean-Eudes Dazard
Reference: Dazard J-E., Saha S., Ewing R. ROCS: a Reproducibility Index and Confidence Score for Interaction Proteomics Studies. BMC Bioinformatics (2012) 13(1):128.

ROCS implements an algorithmic method for inferring Protein-Protein Interactions from Affinity-Purification Mass-Spectrometry data. It is designed to handle difficult problems of accuracy and reproducibility posed by large multivariate AP-MS datasets.