Galaxy |

Cell types - get tool performance table (version 1.1.1+galaxy0)

Input tables:

Classification tables obtained from multiple classisifiers

Reference metadata file:

Metadata file with reference labels

Include Semantic Similarity:

Should semantic similarity be included in calculation of combined score?

Exclusions:

Config file with exclusions

Ontology graph:

Ontology graph to run semantis similarity computations

Label - CL term mapping:

Mapping between cell labels and ontology terms

Reference file barcode field:

Name of barcode field in reference metadata file

Predicted file barcode field:

Name of barcode field in predictions file

Reference label column:

Label column in reference file

Predicted file label column:

Name of label field in predictions file

Semantic similarity metric:

What semantic similarity metric should be used? NB: if include-sem-siml is set to True, make sure to use a metric that is in the [0;1] interval. See https://www.bioconductor.org/packages/release/bioc/html/Onassis.html for more detail.

More information can be found at https://github.com/ebi-gene-expression-group/cell-types-analysis

Version history 0.1.6+galaxy0: Add removing non-alphanumeric characters from labels in metadata files 0.0.5+galaxy0: Initial contribution. Andrey Solovyev, Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/. 0.0.5+galaxy1: Standardise input/output format into .txt.