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Once #17 is done, the next step will be to identify differentially expressed genes on the `BayesSpace` clusters. There are several ways to do this and we currently don't have code for this at `spatial…
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We want to write a new vignette that shows how you can use `spatialLIBD` using the data from https://support.10xgenomics.com/spatial-gene-expression/datasets. I think that it can start with https://gi…
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I'm having trouble with two of the gene sets.
The loaded Scatterstrom data doesn't have the correct column names. Here's the code I run and here's the error I get when trying to create `asd_exome_…
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https://github.com/LieberInstitute/spatialDLPFC
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Hi,
Thanks for organizing the data. I have tried to use the spatialDLPFC_Visium data downloaded using spatialLIBD package. I saw a discussion about the manual annotation in the data. Just want to …
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Hi Ryan,
I believe that either https://github.com/LieberInstitute/spatial_hpc/blob/main/code/11_iSEE_apps/pseudobulk_iSEE or https://github.com/LieberInstitute/spatial_hpc/tree/main/code/11_iSEE_ap…
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It'll be easier to run the spatial registration process in your own data if we have functions for doing something like https://github.com/LieberInstitute/HumanPilot/blob/master/Analysis/Layer_Guesses/…
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Hi BiocFileCache team,
Last week at BioC2023 I ran into some issues with `spatialLIBD::fetch_data("spatialDLPFC_Visium_modeling_results")` and related functions after I wiped out clean my BiocFileC…
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Hello DLPFC_snRNAseq team!
First off, thanks for making this data available and for writing such clean and well-documented code!
I was wondering if you would be able to point me to where I can…
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- https://www.nature.com/articles/s41593-020-00787-0
- http://research.libd.org/spatialLIBD/articles/spatialLIBD.html
- histology available