Galaxy |

Cell types - get consensus outputs (version 1.1.1+galaxy0)

Aggregated tables:

Aggregated prediction tables from multiple tools

Tool performance table:

Table with tools performance metrics

Include Semantic Similarity:

Should semantic similarity be included in calculation of combined score?

Sort by aggregated score:

Should the cells be ordered by aggregated score?

Exclusions file:

Yaml file with trivial terms and unlabelled cells

cl terms mapping:

Label - CL term mapping

Ontology graph:

Ontology graph to run similairty calculations

True Labels:

Path to the true labels tsv file in case tool performance is evaluated. Expected columns: cell_id, true_label, ontology_term

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.