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Hi,
I'm trying to run the tutorial on the striatum dataset but I got this error message:
![Screenshot 2024-06-12 at 3 56 19 PM](https://github.com/Czh3/iSpatial/assets/50332096/d71683d2-b7ba-487…
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Summarize commonly used QC metrics in Single Cell data analysis
* Method 1
* Method 2
* Method 3
Recommended QC metrics/method for spatially-resolved data.
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- download a data of choice from 10x genomics with `sc.datasets_visium_sge()` (you can browse them [here](https://support.10xgenomics.com/spatial-gene-expression/datasets))
- run the scanpy tutorial,…
giovp updated
3 years ago
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### Description of feature
Apparently this is a thing now (e.g. 10x spatial transcriptomics + mixcr, e.g. in [this paper](https://www.sciencedirect.com/science/article/pii/S1074761322000814?via%3Dihu…
grst updated
4 months ago
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Hi,
I'm trying to run graph_peak_caller on a ATAC-seq data which is aligned to a single test chromosome graph which was generated with the PGGB pipeline. After aligning the raw data to the graph us…
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Hello, my data is from the spatial transcriptome. There are three biological repetitions in the experimental group and the control group respectively. Can I use three experimental groups to create a c…
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hello,when i run the demo of Cell-cell_interaction,
`weights_graph, distance_graph, adata = st.tl.weighted_spatial_graph(
adata,
n_neighbors=10,
)`
with error `AttributeError: module 'spa…
xhli2 updated
2 months ago
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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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https://r-spatial.github.io/sf/reference/interpolate_aw.html
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# Overview of 2014 - 2019 DO | Weekly Research Update
After our conversations last week, we decided that it would be best if I focus my attention on mechanistically explaining the spatial and tempora…