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Problem solved
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Hi there. I am uploading files that I downloaded from the Nanostring Geomx DSP Analysis platform but can't get them to be read by GeoMx. I have been trying to de-bug this for a few days now and can't …
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When the `gene_weighting_rule` is provided as an argument to `insitucor`, this is not getting passed on to the step `defineModules`.
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Hi,
I saw that xCell is intended for bulk gene expression. Is xCell suitable for Nanostring GeoMx data to predict cell type enrichment?
Thank you.
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## Description
Nanostring CosMx datasets have a new file export format through TileDB, https://nanostring.com/wp-content/uploads/2023/01/LiverPublicDataRelease.html
They no longer give .csv file…
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Can I ask you a question about reference scale for the Insitutype cell labeling part?
From https://github.com/Nanostring-Biostats/InSituType/blob/main/vignettes/NSCLC-supervised-cell-typing-vignette.…
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Hi Nanostring team,
Will the reference matrices be updated with more genes based on experiments from the 6,000 plex assay? If this is in development, would the 6,000-plex assay matrices allow for t…
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Hello,
When running insitutype() on my data, I get the following error in phase 4:
`phase 4: classifying all 405339 cells
Error in .local(x, ...) : Cells with 0 counts were found. Please remove.…
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Hello, I'm trying to make an ImageDimPlot of Nanostring CosMx data using v5, and keep getting the error "No compatible spatial coordinates present". I followed the vignette but used unsupervised clust…
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Hi, here I tried to register the DAPI staining images between nanostring and xenium, and apply that transformation to the segmentation masks, the images aligns well in the napari, however, when I extr…