Helper Module for Deep Learning.

Module that provides functions to prepare the Kang dataset.

H. M. Kang, et al., Multiplexed droplet single-cell rna-sequencing using natural genetic variation. Nature biotechnology, 2018.

class pynet.datasets.kang.Item(data, trainset, testset, membership_mask)¶

property data¶

Alias for field number 0

property membership_mask¶

Alias for field number 3

property testset¶

Alias for field number 2

property trainset¶

Alias for field number 1

pynet.datasets.kang.fetch_kang(datasetdir, random_state=None)[source]¶

Download the Kang dataset described in [1].

[1] H. M. Kang, et al., Multiplexed droplet single-cell rna-sequencing using natural genetic variation.Nature biotechnology, 2018.

Parameters

datasetdir: str

the dataset destination folder.

random_state: int, default None

controls the shuffling applied to the data before applying the split.

Returns

item: namedtuple

a named tuple containing ‘data’, ‘trainset’, ‘testset’ and ‘membership_mask’.

pynet.datasets.kang.load_annotations(gmt, genes, min_genes=10)[source]¶

pynet.datasets.kang.parse_gmt(path, symbols=None, min_genes=10)[source]¶