search

JEFworks-Lab / STdeconvolve

Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data
http://jef.works/STdeconvolve/
110 stars 13 forks source link

Cell volumes for MPOA reproduction #34

Open paulmorio opened 1 year ago

paulmorio commented 1 year ago

Dear Dr. Miller (@bmill3r ),

Sorry to bother you, I am trying to run through the pseudo synthetic ST data (MPOA) analysis using STDeconvolve MPOA tutorial, but cannot find the cell volume data for animal FN7, datasets 171021_FN7_2_M22_M26 and 171023_FN7_1_M22_M26 in order to get discrete transcipt counts for each of the genes in order to continue with the LDA modelling. Could you perhaps share them?

Best regards, paulmorio

bmill3r commented 1 year ago

Hi @paulmorio,

Sorry for the delay! The files you want should be available here as part of an RData file.

This contains counts_, annot.table_, majorCellTypes, and neuronalCellsubtypes after the preprocessing and filtering. I will need to check the original publication for the cell volume information but this should be what you need to start generating the simulated pixels.

Hope this helps! Brendan

paulmorio commented 1 year ago

Excellent, thank you very much!

xieaq commented 1 year ago

Hi Dr. Miller (@bmill3r ) The link does not exist. Could you perhaps share them again? Thanks!

Best, Aoqi

bmill3r commented 1 year ago

Hi Dr. Miller (@bmill3r ) The link does not exist. Could you perhaps share them again? Thanks!

Best, Aoqi

Link should be fixed: https://drive.google.com/drive/folders/11ip1VreNdD2uBvWgIpMQZ9h00xz7FFKC?usp=sharing

xieaq commented 1 year ago

Hi Dr. Miller (@bmill3r ) The link does not exist. Could you perhaps share them again? Thanks! Best, Aoqi

Link should be fixed: https://drive.google.com/drive/folders/11ip1VreNdD2uBvWgIpMQZ9h00xz7FFKC?usp=sharing

Got it! Thanks a lot!