Galaxy |

Cell types - get empirical distribution (version 1.1.1+galaxy0)

Input reference file:

Text file with reference cell labels

Exclusions file:

YML file with excluded/unlabelled terms

Reference label column:

Label column in reference file

Label - CL term mapping:

Mapping between cell labels and ontology terms

Number of iterations:

Number of simulations to generate empirical CDF

Number of labels to sample:

Number of labels to sample for each permutation

Ontology graph:

Ontology graph to run semantis similarity computations

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.