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Dear Giotto team,
I am trying to Identify DEGs between two selected sets of spots after integration of two Giotto objects
I selected the spots that belonged to the same leiden cluster but they…
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Hello Giotto team,
We try to run "runPAGEEnrich":
F1_normalized_standard_6000 = runPAGEEnrich(gobject = F1_normalized_standard_6000, min_overlap_genes = 0, p_value = TRUE, sign_matrix = PAGE_matri…
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Hi,
I'm following the Mouse Brain Visium [Vignette](https://giottosuite.readthedocs.io/en/latest/subsections/datasets/mouse_visium_brain.html) and is having trouble with the makeSignMatrixDWLSfromMa…
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- [x] Introduction - scope 0.5-1 page
- look into reviews
- broad overview into the field
- mention nature methods "method of the year 2020"
- define axis: targeted/high-resolution vs unbiased…
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> visium_kidney = createGiottoVisiumObject(visium_dir = data_path,
+ expr_data = 'raw',
+ png_name = image_name,
+ …
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Hi Giotto team,
I am using the function of neighborhood analysis, and I really appreciate it. And then I wonder whether we have the function to show gene reads related to distance clearly. Which…
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Where is the "metadata_giotto.csv" in data_preparation.ipynb in nanostring_cosmx_human_nsclc dataset?
I can't find "metadata_giotto.csv" in https://nanostring.com/products/cosmx-spatial-molecular-ima…
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#### Description
When `overlap_fraction` is very small (close to 0) and `n_intervals` is a multiple(?) of the number of points (X.shape[0]), the `fit_transform` step produces a cover, which does not …
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I am sorry for opening many issues and thank you for always helping me out; currently I am trying to run this code (steps 52 on cp_manuscript_code). I also still use the 2020_ST_STCC data.
`combo_…
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thank you for your great package. i use it for spatCellCellcom(). i reference documents(https://rubd.github.io/Giotto_site/articles/mouse_seqFISH_cortex_200914.html).
I encountered an error when rea…