SingleCellAssay

Infrastructure and Tools for Single Cell Assay Analysis

Installation Instructions

 install.packages('devtools')
 library(devtools)
 install_github('SingleCellAssay', 'RGLab')
 # *or* if you don't have a working latex setup
 install_github('SingleCellAssay', 'RGLab', build_vignettes=FALSE)
 vignette('SingleCellAssay-intro')

Needs roxygen2 4.0.0.99 or higher (available on github) if the documentation is regenerated--otherwise the NAMESPACE file will not be correct.

New Features in version .85

• The interface to zlm.SingleCellAssay has changed somewhat, and is not completely backwards compatible
  • But now it is easier to add hurdle models with different modeling functions. Try method='glmer' or method='bayesglm' for mixed effects or bayesian methods.
  • Multiple hypothesis can be tested by passing a list of hypothesis (either terms to drop for Likelihood Ratio Tests, or hypotheses formated a la car::lht
• Thresholding support for NanoString in thresholdNanoString