Galaxy |

Scmap cell projection (version 1.6.4+galaxy2)

Index SingleCellExperiment object:

File with serialized SingleCellExperiment object as produced by 'scmap select features' and 'scmap index clusters', onto which another dataset will be projected.

SingleCellExperiment object to project:

File with serialized SingleCellExperiment object to project onto the index'

Number of nearest neighbours:

A positive integer specifying the number of nearest neighbours to find

Nearest neighbour threshold:

A positive integer specifying the number of matching nearest neighbours required to label a cell.

Similarity threshold:

Threshold on similarity (or probability for SVM and RF).

Annotate cells of the projection dataset using labels of the reference?:

If cell cluster annotation is available for the reference datasets, in addition to finding top 10 nearest neighbours scmap-cell also allows to annotate cells of the projection dataset using labels of the reference.

cluster_col:

More information can be found at https://bioconductor.org/packages/release/bioc/html/scmap.html

Version history 1.6.4+galaxy0: Update scmap-cli to 0.1.0 1.6.3+galaxy0: Update scmap-cli to 0.0.11 1.6.2+galaxy0: Update scmap-cli to 0.0.10 1.6.1+galaxy0: Update scmap-cli to 0.0.9. 1.6.0+galaxy0: Initial contribution. Jonathan Manning, Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/.