fixing broken links and other rmarkdown rendering issues

[kjkrishnan]

• Removed references to {SingleCellExperiment} which didn't render appropriately due to lack of SingleCellExperiment documentation url as well as any attempts to work around rmd formatting limitations (see It doesn't seem that you use standard markdown syntax in your .Rmd files. As a consequence there are many small cosmetic problems with the rendering of the HTML vignettes. See for example \underline{named} vector or {SingleCellExperiment} here #124 )
• Replaced instance of domino2 with updated package name
• Exported print and show methods (see For example, if I run these four lines of code in a fresh R session and try to display the dom object, I get hundreds of screens of output. This is unfortunate because domino objects actually have a show() method whose purpose is to prevent that. But that method is defined in the dominoSignal package and since the package is not loaded the method is not found. Or maybe it's because the package does not export the method, I'm not sure. In any case you need to export that method. #125 )
• Added set.seed calls to vignettes (see I still don't see any set.seed() calls in the HTML vignettes. #126 )
• Consistency checks for terms, spellings, formatting, as well as some proofreading while I was at it

[jmitchell81]

Updates affect only the documentation and vignettes for the package