SCSBrainTypeCollection: Brain Cell Type Marker Collection for anRichment


T. Grant Belgard, Peter Langfelder, Verge Genomics Team




Peter (dot) Langfelder (at) gmail (dot) com


Caution: experimental package!

This package should be considered experimental. The "API" (such as it is), i.e., the function names, arguments and returned values, can and probably will change.

Single Cell Sequencing Brain Cell Type Collection for anRichment

This package contains a collection of gene sets to be used with functions from the package anRichment. This collection contains sets of genes significantly over-expressed in broad cell types identified in single cell sequencing by Zeisel et al., Science (2015).

Manual download and installation

Prerequisites

Although the package can be installed under older R versions, we strongly recommend using the newest R version because the annotation packages are continuously updated.

The SCSBrainCellTypeCollection package requires the package anRichment, and all of its dependecies, to be installed.

R package download and installation

Package SCSBrainCellTypeCollection is available here as source code and pre-compiled versions for Windows and Mac OSX.

Brief documentation available:

For all other platforms and R versions: please either upgrade to the new R (it is worth it), or install the source package.

Installation instructions

Short installation instructions, including other required and recommended packages, are available here.

Problems installing or using the package

Please see the list of Frequently Asked Questions (and frequently given answers); the solution to your problem may already be posted there. If you find a bug in the newest version, please email Peter Langfelder.