https://github.com/mojaveazure/loomr

An R-based interface for loom files
https://github.com/mojaveazure/loomr

hdf5 loom loom-files r single-cell-genomics single-cell-rna-seq

Last synced: about 2 months ago
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An R-based interface for loom files

• Host: GitHub
• URL: https://github.com/mojaveazure/loomr
• Owner: mojaveazure
• Created: 2017-10-20T21:24:06.000Z (about 7 years ago)
• Default Branch: master
• Last Pushed: 2020-07-09T17:51:09.000Z (over 4 years ago)
• Last Synced: 2024-11-01T02:51:47.358Z (2 months ago)
• Topics: hdf5, loom, loom-files, r, single-cell-genomics, single-cell-rna-seq
• Language: R
• Homepage:
• Size: 327 KB
• Stars: 62
• Watchers: 7
• Forks: 16
• Open Issues: 51
• Metadata Files:
  • Readme: README.md

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README

        


# loomR

### An R interface for loom files

For more information on loom files, please see the documentation for [loompy](https://github.com/linnarsson-lab/loompy)

## Tutorial

A tutorial for loomR can be found [here](http://satijalab.org/loomR/loomR_tutorial.html). A full function and method reference can be found [here](http://satijalab.org/loomR/loomR.pdf).

## 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](https://cran.r-project.org/) v3.4.x

 - The [R6](https://cran.r-project.org/package=R6) package

 - The [hdf5r](https://cran.r-project.org/package=hdf5r) package

 - The [iterators](https://cran.r-project.org/package=iterators) package

 - The [itertools](https://cran.r-project.org/package=itertools) package

 - The HDF5 [C++ API](https://support.hdfgroup.org/HDF5/release/obtainsrc.html)

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

| Operating system | Command |

| ---------------- | ------- |

| macOS | Using [Homebrew](https://brew.sh/), `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](https://github.com/mannau/h5-libwin) |