kc-lan / loomr

An R-based interface for loom files

loomR

An R interface for loom files

For more information on loom files, please see the documentation for loompy

Tutorial

A tutorial for loomR can be found here. A full function and method reference can be found here.

Compatability with loompy

loomR aims to be completely compatible with loompy. Currently, loomR implements the following methods of the loompy API:

• map/apply
• create
• connect
• combine
• subset
• add layer
• add attriute
• add graph
• add cells
• add loom

Dependencies

loomR depends on:

• R v3.4.x
• The R6 package
• The hdf5r package
• The iterators package
• The itertools package
• The HDF5 C++ API

To get the HDF5 C++ API, please see the table below:

Operating system	Command
macOS	Using Homebrew, brew install hdf5
Debian and Debian-based OSes	sudo apt install libhdf5-dev
Red Hat-based OSes	sudo dnf install hdf5-devel or sudo yum install hdf5-devel
Windows	Download precombiled binaries from Mario Annau here