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Hello!
We currently have CODEX data after segmentation in HALO. I was curios, if there is a way to use this segmentated dataset for further downstream analysis at the IMC data analysis workflow , f…
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## Problem Statement
It is possible to plot the expression data using `plotSpot`. Nevertheless, it involves manipulating the `SpatialExperiment` object by creating a new column in the `colData`. The …
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Installation would not complete. I tried a few things, including setting `dependencies=TRUE` but I think it was creating a separate prior install of GSVA via `BiocManager::install("GSVA")` that may ha…
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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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Currently `run_app()` has the argument `image_path` at https://github.com/LieberInstitute/spatialLIBD/blob/49d0735a779211da86e8efb119fd6872e3960c81/R/run_app.R#L57 which then is used at https://github…
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您好，我刚重新安装的Mime包，包括依赖的包。用自带数据进行分析，然后我运行函数
auc.other.pre
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Hi,
I have been trying to access the raw data provided in the spatialLIBD package. So far, I have used:
```
# as specified in the vignette
sce
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> # ------ start clustering block ---------
bank
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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/phipsonlab/spaceMarker
Confirm the following by e…
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## The multi-gene function fails if the genes requested report no expression variation in some slides (samples).
I have encountered an exception when certain genes are not present in some slides.…