Inferelator 3.0 Yeast Single-Cell Benchmarking Data

Yeast single-cell gene expression data, database-derived prior knowledge network, and hand-curated gold standard network. Used to benchmark the Inferelator 3.0, SCENIC, and CellOracle.

Expression data (GSE144820_GSE125162.tsv.gz) is an integer count matrix [44343 rows x 6763 columns] with an index column (0) assembled from GSE144820 and GSE125162. Included is a paired metadata file (GSE144820_GSE125162_META_DATA.tsv.gz).

A database-derived prior knowledge network (YEASTRACT_20190713_BOTH.tsv) is a boolean connectivity matrix [6885 rows x 220 columns] with an index column (0) obtained from the YEASTRACT database on 07132019. It consists of edges which have both DNA localization evidence and evidence of changes to gene expression after TF perturbation.

A curated gold standard network (Tchourine_2018_yeast_gold_standard.tsv) is a signed connectivity matrix [993 rows x 98 columns] with an index column (0). Details of its construction have been published.