This series of files was used to update BrainPalmSeq, a curated database of RNA-seq studies for palmitoylating and depalmitoylating enzymes, with data from the Brain Initiative Cell Census Network (BICCN) 2.0 data release available online at the Allen Brain Cell Atlas and published as Yao, Z., van Velthoven, C.T.J., Kunst, M. et al. A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain. Nature 624, 317–332 (2023). https://doi.org/10.1038/s41586-023-06812-z.
ABC outputs/ contains the counts pulled from the BICCN 2.0 data release as per Allen Brain Cell Atlas gene expression data download instructions.
R contains R scripts to add descriptors from the Allen Institute Common Cell Type Nomenclature as metadata in downstream visualizations and to prepare the data for processing in the Python notebooks.
csv contains text files generated by the R scripts. These are the input files for the Python notebooks.
Python Notebooks contains Jupyter Notebooks meant to generate the Bokeh visualizations.
HTML outputs contains the outputs of the Jupyter Notebooks that were used to generate the visualizations on the website.
- @thompsand pulled data from Allen Brain Cell Atlas, generated R scripts, adapted Python Notebooks for analysis, and updated the website.
- @Peter-Hogg wrote the templates for the Jupyter Notebook.
We would like to thank the Allen Institute for making this dataset publically available and the laboratory animals who made this dataset possible.