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It would be fantastic if measureObjects expanded the information in mcols of the masks/images into the colData of the resulting SingleCellExperiment/SpatialExperiment.
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Hi everyone,
in the new Space Ranger V2 there have been changes to the output file definitions, causing an error when loading spatial data created with the new pipeline version with `read10xVisium…
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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/Nina-Song/stJoincount
Confirm the following by ed…
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Hi all,
Will you accept a PR on `suite` for conversion between the Bioconductor *Experiment classes?
I've hacked this together for my work and it doesn't seem too hard to generalize... maybe.
…
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Hi there. Thank you for spacexr, I've found it very useful in my work.
My question is regarding the function plot_cond_occur()
I was hoping to compare two experimental conditions by looking at h…
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**Goal**
User asks if it is possible to see multiple PCA or UMAP scatterplots of the same data but with different cell set labels. So for a given dataset with 2 cell set metas, ie Tier 1, and Tier 2…
lee-t updated
2 years ago
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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/SydneyBioX/Statial
Confirm the following by editi…
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Hi @nilseling,
as discussed here the issue report for the `buildSpatialGraph` function. In principle, I tried to create a k-nearest neighbor graph (k=10, max_dist = 30) for a subset of my sce (her…
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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/SydneyBioX/scFeatures
Confirm the following by ed…
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Update input arguments to allow non-SpatialExperiment inputs, i.e. matrices of logcounts and spatial coordinates.
This will make the method more broadly accessible, e.g. by Seurat or Python users.