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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/peicai/DESpace
Confirm the following by editing e…
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This will be done only with the n = 4 Visium IF samples. It will depend on results from several other issues https://github.com/LieberInstitute/spatialDLPFC/issues?q=is%3Aissue+is%3Aopen+label%3Aspot-…
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Hello, can you provide the data for analysis in visium_human_dorsolateral_prefrontal_Cortex.r?
I can get the raw data, but I'm not sure what goes from the raw data to the data for your analysis.
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Identify top spatially variable genes (SVGs) using SPARK-X
Notes:
- During exploratory analyses we tried SPARK, which does not scale well - update using SPARK-X instead
- Check top n genes to see…
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dear sir,
I have some trouble in running initHMRF_V2 this function, what i am suprised is i have met none problem before running this funtion. Here are the problems I encountered:
hmrf=initHMR…
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Dear bayestme developers,
I am having hard time to interpret plots from bayesTME plot_spatial_expression.
The plots from bayestme seems to be completely reversed to the plots from seurat featurepl…
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Hi! I found some issues of the BOOST.GP function.
1. Could you please change the default setting of n.iter from 10000 to 2000 in order to reduce the running time of it?
2. I tried BOOST.GP on seve…
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/jingeyu/CTSV
Confirm the following by editing eac…
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Hello Jean & team,
I have 10x Visium Spatially resolved RNA seq dataset analyzed with Seurat and would like to try Meringue to compute spatial correlation test across spatial spots with cell type …
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**motivation:**
In principal, `spatialCoords` are not different from reduced dimensions in that they are a numeric matrix with coordinates for each observation. Then again, they are not *reduced di…