We are pleased to announce two new features in MapMyCells.
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MapMyCells now allows users to map data onto the Consensus Basal Ganglia taxonomy, a multi-species (human, macaque, marmoset) taxonomy of cell types in the basal ganglia developed by BICAN’s Human and Mammalian Brain Atlas consortium.
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MapMyCells can now map data collected in one species onto a taxonomy defined in another species. This means users are free to, for instance, submit rat data and map it onto any of our mouse or human taxonomies (or the new Consensus Basal Ganglia taxonomy).
When you submit your data, MapMyCells will compare the gene labels in your dataset to known gene labels published by ENSEMBL and NCBI, infer what species your data was collected from, and then use the ortholog table published by NCBI to find orthologous genes in the reference species. Mapping will proceed as though the genes in your dataset were those orthologous genes. All of this is handled automatically using the new mmc_gene_mapper library. To see a programmatic example of mapping data from one species (rat) onto a taxonomy defined in another species (mouse), see this Jupyter notebook.
More information about MapMyCells input file requirements can be found on this page.
For additional help getting started, checkout our Step-by-Step Guide to Using MapMyCells.
As always, thank you for being part of the AIBS community. Please let us know how we can improve MapMyCells to better serve your needs.