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Trying to change colors in the DEenrichRPlot plot with the "col" argument, but it does not work
```r
DEenrichRPlot(Seurat_object, ident.1 = "KO", ident.2 = "WT", max.genes = 300, enrich.database…
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> visium_kidney = createGiottoVisiumObject(visium_dir = data_path,
+ expr_data = 'raw',
+ png_name = image_name,
+ …
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Hi I am trying to load some 10x Visium data using TENxVisiumList, but am not able to load the data at all. I have verified that the data is there and in the correct form:
> file.exists("/Users/adi…
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The data come from SFEData ... using SpatialFeatureExperiment, try
```
library(SFEData)
library(RBioFormats)
fp import(tt)
Error in rhdf5::h5read(path(x), paste0(group, x@ranges), …
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**Describe the bug**
Currently, the [addClusters](https://www.archrproject.com/reference/addClusters.html) parameter 'method' which can be specified as Seurat or Scran, is the same parameter name as …
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Hi, @bmill3r
Sorry to trouble you. I'm new to analyzing spatial transcriptomes. I am trying to do it with your tools to deconvolve. I have two questions.First, I see the tutorial in “https://github…
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Hi MILO Lab,
Thanks _so_ much for a wonderful tool. I'm hoping to use the Spatial Trajectory screen on a Visium V2 dataset (pre-processed with Seurat and converted to a SPATA2 object using the asS…
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Hello,
Since fetch_data returns error on my machine, I manually downloaded data from the https link for `type == "sce"` in the fetch_data() function and converted the downloaded sce to spe using `…
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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/vjcitn/xenLite
Confirm the following by editing e…
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I feel like it's less confusing for readers/users to have the same section headings in both the manuscript and the docs here when following the package.
1. change `Preparing Images for Fiji` in http:/…