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Hi, I saw mention of a wiki for VISINITY but do not see it in the repo. Is that or other user documentation available?
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Thank you so much for creating this wonderful tool. I am utilizing spatialdecon to estimate the cell fractions of each spatial spot in my visium 10x tumor sample.
from reading your vignette there s…
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Dear developers,
I'm trying to identify a fusion break that seems to occur in introns with a very very low expression value. I have only 7 read pairs out of 15 million read pairs for the fusion gene.…
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I'm trying to perform `SpatialDecon` on GeoMX DSP data prior filtered following the [NanoString R guide](https://bioconductor.org/packages/devel/workflows/vignettes/GeoMxWorkflows/inst/doc/GeomxTools_…
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## Erroneous examples
When calling `negativeControlSubset` in a function, it returned errors like below
```
Error in subset.default(x = new("NanoStringGeoMxSet", dimLabels = c("TargetName", :
…
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- [x] Dave asked marketing about the poster session (from the sponsorship)
- [x] Data: Kidney WTA data (GEO script hub)
- [x] Vignettes: dev
- [x] Update the dev on Bioconductor (Nicole) (in prog…
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Hi-
I want to use the `heatmSpatialCorFeats` but did my initial analysis in v 1.1.0 and the function (from what I can tell) is only newly present. I've upgraded my Giotto version to 3.3.0 but due t…
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From your earliest SMI ReadMe file (https://nanostring-public-share.s3.us-west-2.amazonaws.com/SMI-Compressed/SMI-ReadMe.html), the conversion factor for pixel to uM was 0.18. This was used as a guide…
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with stereoseq and single cell raw counts data, I got the error: NotImplementedError: The Cell2location model currently does not support minified data., But the data I use is the raw counts
## Ple…
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The following are edits from Rpackages missing from NCTools
**Autoplot:**
- [ ] Add the function shiftfromzero to the beginning of ercc-lod. This function is in 360 so will need to define as well…