r-bioc-qusage

qusage: Quantitative Set Analysis for Gene Expression

This package is an implementation the Quantitative Set Analysis for Gene Expression (QuSAGE) method described in (Yaari G. et al, Nucl Acids Res, 2013). This is a novel Gene Set Enrichment-type test, which is designed to provide a faster, more accurate, and easier to understand test for gene expression studies. qusage accounts for inter-gene correlations using the Variance Inflation Factor technique proposed by Wu et al. (Nucleic Acids Res, 2012). In addition, rather than simply evaluating the deviation from a null hypothesis with a single number (a P value), qusage quantifies gene set activity with a complete probability density function (PDF). From this PDF, P values and confidence intervals can be easily extracted. Preserving the PDF also allows for post-hoc analysis (e.g., pair-wise comparisons of gene set activity) while maintaining statistical traceability. Finally, while qusage is compatible with individual gene statistics from existing methods (e.g., LIMMA), a Welch-based method is implemented that is shown to improve specificity. For questions, contact Chris Bolen (cbolen1@gmail.com) or Steven Kleinstein (steven.kleinstein@yale.edu)

virulencefinder

identify virulence genes in total or partial sequenced isolates of bacteria

The VirulenceFinder service contains one Python script virulencefinder.py which is the script of the latest version of the VirulenceFinder service. VirulenceFinder identifies viruelnce genes in total or partial sequenced isolates of bacteria - at the moment only E. coli, Enterococcus, S. aureus and Listeria are available.

pre-commit

Git pre-commit hook framework

A framework for managing and maintaining multi-language Git pre-commit hooks.

libotbrcc8-6.0-1

ORFEO Toolbox library - OTBRCC8

libotbcommon-6.0-1

ORFEO Toolbox library - OTBCommon

node-normalize.css

Modern alternative to CSS resets

Normalize.css makes browsers render all elements more consistently and in line with modern standards. It precisely targets only the styles that need normalizing.