Interfacing Seurat with the R tidy universe

Declutter your R workflow with tidy tools

The R language has withstood the test of time. Forty years after it was initially developed (in the form of the S language) R is being used by millions of programmers on workflows the inventors of the language could never have imagined. Although base R packages perform well in most settings, workflows can be made more efficient by developing packages with more consistent arguments, inputs and o...

rtracklayer: an R package for interfacing with genome browsers

SUMMARY The rtracklayer package supports the integration of existing genome browsers with experimental data analyses performed in R. The user may (i) transfer annotation tracks to and from a genome browser and (ii) create and manipulate browser views to focus on a particular set of annotations in a specific genomic region. Currently, the UCSC genome browser is supported. AVAILABILITY The pack...

On P4-tidy graphs

We study the P4-tidy graphs, a new class defined by Rusu [30] in order to illustrate the notion of P4-domination in perfect graphs. This class strictly contains the P4-extendible graphs and the P4-lite graphs defined by Jamison & Olariu in [19] and [23] and we show that the P4-tidy graphs and P4-lite graphs are closely related. Note that the class of P4-lite graphs is a class of brittle graphs ...

Death of Seurat

Database and R Interfacing for Annotated Microarray Data

A framework for expression data repositories (MAGE-ML compatiblity) emerged during the last years. Focus is now shifting towards the integration of expression databases into genomic and other bioinformatic database system as well as with statistical analysis platforms. We present an implementation of such a repository system at MIPS (http://mips.gsf.de/). An important requirement for this integ...