An R package (compatible with SCope) to create generic .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters and markers, ... The package can also be used to extract data from .loom files.
- HDF5 >= 1.10.1
For Linux and MacOS machines, version 1.10.1 can be installed with this snippet:
curl -O https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.1/src/hdf5-1.10.1.tar
cd hdf5-1.10.1
./configure
make -j4
make check
make install
To install HDF5 on a Windows machine, please use the prebuilt binaries available at https://www.hdfgroup.org/downloads/hdf5/.
For other HDF5 releases, please visit https://support.hdfgroup.org/ftp/HDF5/releases/.
Installation should take less than one minute.
install.packages("devtools")
library(devtools)
install_github("aertslab/SCopeLoomR")
You can find a tutorial on how to create .loom files and extract data from them here.
November 8, 2018
-
Version 0.3.1
- Fix bug when adding sparse matrices.
-
Version 0.3.0
- Add feature to extract the gene expression matrix of a given cluster.
- Update tutorial.
October 31, 2018
- Version 0.2.2
- Add sanity tests when adding embeddings and SCENIC regulons with threshold assignments.
- Small bug fixes.
August 8, 2018
- Version 0.2.1
- Fix encoding bug leading to annotation not shown in SCope.
- Add sanity test to check that all cells from the dgem are present in the Seurat clusters.
July 6, 2018
- Version 0.2.0
- Add feature to store trajectory data. Currently, the following softwares can have their trajectory data easily stored in .loom files:
monocle.
- Add feature to store trajectory data. Currently, the following softwares can have their trajectory data easily stored in .loom files:
July 4, 2018
- Version 0.1.0
- Add feature to store metrics