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.