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# General Notes
This repository serves as a mostly automa…
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Hi Jan,
I am using SPATA2 on a Xenium dataset .
I want to create a spatial trajectory in the image to view the spatial distribution of specified cell types.
But currently the ”createSpatialTrajecto…
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## Problem
**Is your request related to a problem? Please describe.**
There is a lack of clarity and standardisation in how IfcSpatialZone is being used and implemented in various software tools…
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In the preliminary version of the practical 1, I try to cover following topics:
- [ ] Introduction to Imaging-Based Spatial Transcriptomics (Xenium Platform)
- Overview of Xenium technology and it…
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I have finished an power spectrum density analysis recently by using .spectral(), and making significant analysis by using .signif_test(). However, I'm facing a problem about how I could plot optional…
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Hi,
Thanks for the great package.
I was running spacemake with visium data, and got an exception:
rule run_automated_analysis:
input: projects/visium_demo/processed_data/DSG_Control/illumi…
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Hello, How can I get a copy of the RData that you use in the Spatial vignette?
https://github.com/jinworks/CellChat/blob/main/tutorial/CellChat_analysis_of_spatial_transcriptomics_data.Rmd#L68
…
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Trying to use BPCells to help with smoother analysis of Visium HD data but keep getting errors.
localdir visium_data
> # Convert to BPCells format
> expr_matrix expr_matrix_int
> write_ma…
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Hi all! In a couple of weeks, I'd like to follow up Jamie's recent **R spatial workshop** with round 2, in which we will focus on manipulating vector spatial objects, especially polygons and shapefil…
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Hello,
Thank you for developing such an effective tool. I am a researcher just starting spatial transcriptomics analysis with CosMx. I have successfully uploaded my CosMx h5ad data into Cirrocumulu…