Software

Plethy (Bottomly et al 2015 BMC Bioinformatics): R/Bioconductor framework for pre-processing and analysis of plethysmography data with emphasis on larger scale longitudinal experiments. The plethy plethy package was designed to facilitate quality control and exploratory data analysis. DOI: /10.5281/zenodo.12570

oligoMask (Bottomly et al 2014, R Journal): Tools for masking out problematic Affymetrix probes using VCF files and the oligo Bioconductor package. DOI:10.5281/zenodo.12571

HitWalker Version 1 (Bottomly et al. 2013): Framework to prioritize patient variants relative to their weighted proximity to functional assay results in a protein-protein interaction network. It is highly extensible, allowing incorporation of diverse data types to refine prioritization. In addition to a ranked list of variants, we have also devised a simple shortest path-based approach of visualizing the results in an intuitive manner to provide biological interpretation.

ProCoNA (Gibbs et al 2013): Protein co-expression networks allow novel approaches for biological interpretation, quality control, inference of protein abundance, a framework for potentially resolving degenerate peptide-protein mappings, and a biomarker signature discovery.

POD (Bottomly et al 2013): Approach for patient-specific outlier detection.

Concordance Workbench (Bottomly et al 2010 NAR): Approach to combine ChIP-seq results from different peak-finding algorithms in order to assess concordance among the approaches and identify high-confidence peaks.

SNPMask (Walter et al 2007 Nature Methods): Computational mask to filter out SNPs that impact hybridization-based techniques when non-reference samples are being examined on standard manufacturer arrays.

Consense (Laderas and McWeeney 2007, OMICS): A consensus framework for exploring functional genomics data using multiple clustering methods

Tandtraq (Laderas et al 2007, Bioinformatics): An open-source tool for integrated protein identification and quantitation.