BICCN Mouse MOp meta-markers

We extracted replicable markers for neuron cell types from a compendium of 7 scRNAseq datasets generated by the BICCN in the mouse primary motor cortex (https://doi.org/10.1101/2020.02.29.970558). The markers were extracted using the MetaMarkers package (https://github.com/gillislab/MetaMarkers) using default parameters and keeping the top 1000 markers for each cell type.<br>We present markers for cell types at each level of the hierarchy defined by the BICCN. - biccn_class_markers.csv: highest level with only 3 cell types (excitatory neurons, inhibitory neurons, non-neurons). - biccn_subclass_markers.csv: intermediate level containing 13 cell types (e.g. PV+ interneurons, L6b excitatory neurons). - biccn_cluster_markers.csv: high-resolution level containing 86 cell types (e.g. Chandelier cells).<br>The number of informative markers varies by cell type. To find the best number of markers, we looked for optimal annotation performance for each cell type. The results are summarized in "optimal_number_markers.csv". For each cell type, performance is reported in column "f1" (0.75 indicates good performance, 1 is perfect performance). To read this table, pick a cell type of interest, find optimal performance, then the range of genes that lead to optimal performance. For example, Chandelier cells (Pvalb Vipr2_2) are perfectly characterized by 50 to 200 markers (F1&gt;0.99).