scrattch.hicat

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I think the install instructions are missing installing WGCNA from bioconductor? They say "several dependencies, including two from BioConductor and one from Github", but only list limma from bioconductor, and...

tmchartrand

to deal with the case map.dat does not have all.markers.

leechangkyu

Hi, What does cl>49 mean after iter_clust? Because the annotation from Tasic 2016 only covers 0-49 clusters, cl>49 cannot be annotated. My sample size is around 20k cells. This is...

yeetingc

Details on the clustering method

2

Hello, I used scrattch.hicat for my scRNA-seq analysis and I thank you for the developpement of this great tool. However, In the pipeline that you used in the Tasic et...

rmathieu25

Constellation plots: calculating knn in reduced dimension space - pca or umap?

3

Hi scrattch.hicat team, I've been trying make some constellation plots of my own using the code in your package. In your methods section for the Yao 2020 preprint, you describe...

carmensandoval

How to cite scratch.hicat ?

1

I've used some of your code for my own research and I'm trying to find a way to reference your package. Could you please point me to the correct reference?...

carmensandoval

Hi Im trying to run the scrattch.hicat module on some 10x data. however the iter_clust function keeps failing with the error Error in unique.default(cl) : unique() applies only to vectors...

deevdevil88

Recommended by Fahimeh: We should build a workflow showing which functions are used for each step of analysis, analogous to our supplementary figure.

hypercompetent

Add this to function as it is required for later steps: row.names(ref.cl.df)

tebakken

Add return.markers = TRUE as default setting to run_consensus_clust. Markers are needed for generation of consensus matrix so function breaks.

tebakken