Code for reproducing the analyses presented in Signature morpho-electric properties of diverse GABAergic interneurons in the human neocortex. It includes the following files:
- complete_patchseq_data_sets[1/2].Rdata - These are R objects that (together) have all of the gene expression data and relevant cell metadata used for analysis. These files must be merged before use, as described in "scripts_gene_expression".
- vgic_genes.csv - This is a manually curated table of voltage-gated ion channels.
- dbc_calb1_ADGRG6.csv - This is the set of cells in the paper that map to Inh L1-3 SST CALB1 or Inh L3-5 SST ADGRG6 along with a call of whether or not they have double bouquet cell morphology.
- acute.culture.locked_sstcalb1.ephys.csv - A set of electrophyisological properties for all patch-seq cells in this study that were mapped to the "Inh L1-3 SST CALB1" cluster.
- cell_morphology_predictions_CALB1.csv - A table of morphologies and predicted morphologies for the same cells mapped to the "Inh L1-3 SST CALB1" cluster.
- DataS1_Donor_table.csv -
- DataS2_micorglial_signature_genes_generalized -
- LeeDalley_ephys_fx.csv
- LeeDalley_manuscript_metadata.csv
- LeeDalley_morpho_features.csv
Most of the data for this manuscript are located in the "data" folder above. In addition you will need to download some larger data files from the Allen Brain Map, as described in the relevant scripts. Additional project information and links to raw data are included in the paper.
Scripts for reproducing most of the analyses presented in this paper are available in the "scripts_**" folders above, which are described in the README for the relevant folders.
The license for this package is available on Github at: https://github.com/AllenInstitute/human_patchseq_gaba/blob/master/LICENSE
This code will be updated only if figures change during review or if corrections need to be made.
If you contribute code to this repository through pull requests or other mechanisms, you are subject to the Allen Institute Contribution Agreement, which is available in full at: https://github.com/AllenInstitute/human_patchseq_gaba/blob/master/CONTRIBUTION