roanvanscheppingen

DESeq2 mentioned in Vignettes

1

DESeq2 doesn't have native support anymore according to #2938 Although it is still mentioned in the Vignette for Psuedobulking, in which it still can be used. I think it would...

Currently the 'standard' export does not contain the polygon information in the 'spatial' layer, nor the transcript locations. I've been looking into ways to import this layer from a polygons.csv...

I think your FAQ mentions the wrong conversion factor for Cosmx data (or Cosmx has changed their conversion). The 'expt.config.txt' of a Cosmx run mentions: `ImPixel_nm: 120.280945` which would translate...

Populuation of cell_metadata is not exactly the same

2

The population column of cell_metadata describes the number of transcripts per cell. However, this differs from the transcript_metadata file. Cell 0, population = 1185 -- transcripts in counts 1218 --...

Cell information not transferred

1

In CosMx data, the initial file contains a cell_ID column and a cell columns. This cell column is unique over all fovs. Cosmx starts recounting cell IDs per FOV. Hence...

Shifting centroids / originals not reported

1

Adding onto #17 is the difficulty to try to find back the same cells in a proseg run compared to an initial Cosmx run. I use the x-global-px and y-global-px...

stitch-cosmx.jl is not working

3

Not familiar with julia, but it's not working. Using `julia stitch-cosmx_RVS2.jl ../../rp_5/image_data/cosm03_images/MsBrainTMA/20240229_204141_S1/ transcripts.csv.gz` ``` ERROR: LoadError: BoundsError: attempt to access 0-element Vector{String} at index [1] Stacktrace: [1] getindex @ ./essentials.jl:13...

Hi, I've been working on analysis of spatial data. It consists out of multiple TMAs of tissue on a single slide, consisting out of 2 conditions. I integrate the data...