-
The basic idea: to differentiate between closely-related cell types, we should re-run insitutype using only relevant genes, not the whole panel.
Rough workflow:
1. run insitutype under whatever w…
-
Dear Dr. Song,
First off - very exciting approach and really nice system.
I saw your preprint the other day and was interested in applying it to some of the example data that you link to for n…
-
I'm currently working with NanoString GeoMx ome.tiff whole-slide IF images containing the following four channels: FITC, Cy3, TexasRed, and Cy5. Ideally, I would want to use MCMICRO as the end-to-end …
-
Currently, InSituType takes only raw count matrices. This is logical, since scaling or transforming data might differ per dataset. However, the inability to take count matrices consisting out of float…
-
Hi,
I was coming across a lot of missing FOVs and saw you recently updated proseg to 1.0.6 which has some more operability with CosMx data and may help with the issue (#26 ), however I run into an …
-
When I run `create_profile_matrix` with a `mtx` object that needs to be transposed (internal to the function), I get the following error:
```
[1] "Transposing Matrix"
Error in t.default(mtx) : argu…
-
- precalculate a matrix of prevalance of gene-gene pairs in pubmed hits
- could color edges of network by pubmed score
- the goal: discern between spatial cors that are expected vs. novel
-
It's currently awkward to identify individual modules on the network plot. Implement a view where this is possible.
Options:
- instead of showing all gene names, only show genes from specified mod…
-
Hello,
I’m trying tor run the analysis on GeoMx data following the guide here: https://bioconductor.org/packages/3.14/workflows/vignettes/GeoMxWorkflows/inst/doc/GeomxTools_RNA-NGS_Analysis.html#
…
-
Hi,
Congratulations for this amazing work.
I ran the NSCLC model on nanostring NSCLC data. The output seems to have visible lines in the borders of overlapping patches. Do you have any suggestion? I…