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DLPFC_snRNAseq
snRNA_seq portion of the spatialDLPFC project
http://research.libd.org/spatialDLPFC/
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Cluster nuclei
#6
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lcolladotor
closed
2 years ago
lcolladotor
commented
2 years ago
After #5,
[x] Cluster using
walktrap
like at
https://github.com/LieberInstitute/10xPilot_snRNAseq-human/blob/master/10x_DLPFC-n3_step02_clust-annot_LAH.R#L142-L143
.
[x] Potentially use
k = 10
, but could compare against
k = 20
. Compare by number of nuclei per spot (we don't want super tiny clusters)
[ ] Consider using the hierarchical clustering approach to further group these clusters (or use
igraph::cut_at()
) like at
https://github.com/LieberInstitute/10xPilot_snRNAseq-human/blob/master/10x_DLPFC-n3_step02_clust-annot_LAH.R#L191-L272
[ ] EDA of cluster results
After #5,
walktraplike at https://github.com/LieberInstitute/10xPilot_snRNAseq-human/blob/master/10x_DLPFC-n3_step02_clust-annot_LAH.R#L142-L143.k = 10, but could compare againstk = 20. Compare by number of nuclei per spot (we don't want super tiny clusters)igraph::cut_at()) like at https://github.com/LieberInstitute/10xPilot_snRNAseq-human/blob/master/10x_DLPFC-n3_step02_clust-annot_LAH.R#L191-L272