Example: Loom file

Loom files are becoming a common way of sharing single cell transcriptomic data. In a loom file, a counts table, a samplesheet, and a featuresheet are kept together inside a single file with an extension .loom. singlet supports reading from loom files via config files.

Your singlet.yml must contain a section such as:

datasets:
 ds1:
   path: xxx.loom
   format: loom
   axis_samples: columns
   index_samples: Cell
   index_features: Gene

Then you can load you Dataset easily:

from singlet.dataset import Dataset
ds = Dataset(dataset='ds1')

To export a Dataset to a loom file, you can use the method to_dataset_file:

from singlet.dataset import Dataset
ds = Dataset(dataset='ds1')
ds.to_dataset_file('xxx.loom')