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Swarbricklab-code / BrCa_cell_atlas

Data processing and analysis related code associated with the study "A single-cell and spatially resolved atlas of human breast cancers".
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Request for gene_clusters.txt file for AUCell analysis for spatial data #23

Closed tahseen-igib closed 1 year ago

tahseen-igib commented 1 year ago

Hi

Thanks for providing the codes for your interesting paper However I am stuck at AUcell analysis for spatial data where i am not able to find file used for temp_metagenes. temp_metagenes <- read.delim("/share/ScratchGeneral/sunwu/projects/MINI_ATLAS_PROJECT/Sept2019/11_visium_brca_metagenes/gene_clusters.txt")

https://github.com/Swarbricklab-code/BrCa_cell_atlas/blob/main/spatial_analysis/brca_gene_module_spatial_AUCell.R

It would be really a great help if you can provide the file.

Thanks!

johnyaku commented 1 year ago

Hi @tahseen-igib.

I've uploaded gene_clusters.txt to the spatial_analysis/ directory of this repo, and adjusted the path in brca_gene_module_spatial_AUCell.R.

There are a number of other hard-coded paths that you may need to adapt for your platform. Most of the data files that these reference can be generated by other scripts in the repo, but if you come across other missing data then please let us know.