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Monocle3 top markers (version 0.1.5+galaxy0)
Input file with monocle3 object cds3 in RDS
(Optional) Set of cells to be considered as reference for marker significance test. Accelerates the marker significance test at some cost in sensitivity.
File with cells to be used as reference cells.
Filters the markers test result by this fraction of expression
The number of top marker genes to report in plots and in top markers list
how many genes of the top ranked specific genes by Jenson-Shannon, to do the more expensive regression test on
Cell groups, choose from 'cluster', 'partition', or any categorical variable in `colData(cds)`
whether to assess the discriminative power of each marker through logistic regression. Can be slow, consider disabling to speed up top_markers().
whether to generate the full markers list as well.
whether to generate the top markers plot.

Monocle3 top markers genes

Identify the genes most specifically expressed in groups of cells. See inline help for options.

More information can be found at https://cole-trapnell-lab.github.io/monocle3/ and https://github.com/ebi-gene-expression-group/monocle-scripts

Version history 0.1.5+galaxy1: Updated to monocle3-cli 0.0.9 for plot cells to allow for multiple genes plotting.

0.1.5+galaxy0: Updated to monocle3-cli 0.0.8 to add top marker genes and fix container plots for plotCells (only those two modules upgraded).

0.1.4+galaxy0: Updated to monocle3-cli 0.0.7 to fix bug with column headers in tsv.

0.1.3+galaxy0: Updated to monocle3-cli 0.0.5 to fix bug with tsv inputs.

0.1.2+galaxy0: Initial version based on monocle3-cli 0.0.3 and monocle3 0.1.2