I have been working with various single nuclei RNA sequencing datasets generated from post-mortem human brain, I would like to compare the analysis workflow I am using currently to that used in Hodge et al 2019 https://doi.org/10.1038/s41586-019-1506-7. Is this code already posted somewhere? If not, would it be possible to make the general analysis pipeline available (e.g. from sequencing read mapping and transcript quantification, through to assignment of cell type to identified clusters)? Thank you for your wonderful resources!
Thanks for your question! You can find the code and data used to produce the figures in the Hodge et al. 2019 manuscript here: https://github.com/AllenInstitute/MTG_celltypes and you can find the Allen Institute’s iterative clustering pipeline here: https://github.com/AllenInstitute/scrattch.hicat.
Thank you so much!