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sdata
SpatialData object
├── Images
│ └── 'morphology_focus': DataTree[cyx] (5, 34119, 39776), (5, 17059, 19888), (5, 8529, 9944), (5, 4264, 4972), (5, 2132, 2486)
├── Labels
│ ├── …
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I have used Seurat a lot for 3' GEX data, but am trying to start using this for Visium spatial transcriptomics. As the title above suggests, I'm trying to run [the VisiumHD data vignette](https://sati…
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Thank you for the great method!
Regarding this algorithm, I'd like to ask whether it is suitable for spatial transcriptomic dataset, such as 10x Genomics Spatial Transcriptomics. If applicable, do …
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Hi David, I am currently running orthofinder on my pc and the program returns some errors iteratively. I am using orthofinder 2.5.4
on conda architecture right now.
Checking required programs ar…
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Hi, I am new to programming and this is my first time posting an error like this, so if there is anything I forgot to include or did wrong please let me know.
I am performing a Trinity run which h…
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Define minimal data, based on the transcriptomics metadata/ontologies found (see #75 ) for different levels:
- shallow (e.g. disease) - not necessarily transcriptomics specific
- data type specifi…
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We are certain that we will be receiving a new data type. Spatial Transcriptomics ([the specific technique](https://spatialtranscriptomics.com/)) will be carried out by Anna Wilbrey-Clark (Sanger). Th…
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Hi there!
I've read about updating this software to handle spatial transcriptomics data and seen the posts suggesting that it would be possible to run this with a spatial dataset, I was wondering …
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issues are:
- [ ] use of compact URI for gene, transcript, exon identifiers
- [ ] use of compact URI for sample identifiers / experimental conditions
- [ ] explicit declaration of `quantitation t…
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# Context
@jahilton reported the case in [**#cell-science-platform**](https://czi-sci.slack.com/archives/C06AVGFV222/p1712859564920389).
This issue depends on [Add modality](https://github.com/…