SpatialExperiment

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Thanks for creating and maintaining the package. I'm experimenting the `SpatialExperiment::read10xVisium`to import the Visium HD data via https://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-libraries-of-mouse-brain-he. I noticed in this example data, specifically default Spaceranger output `square_008um_outputs.tar.gz` (unzipped...

boyiguo1

add functions readXeniumSPE(), readCosmxSPE(), readMerscopeSPE(), and example data

9

Hi there, I tried using MoleculeExperiment (ME) read in these new imaging technology data and coerce them to SPE, but the process is a bit long and bulky. Here these...

estellad

feat: check existence instead of equality for colnames of imgData

22

This simple change lifts the restriction of requiring exactly four columns in `imgData` with names being `c("sample_id", "image_id", "data", "scaleFactor")`. Instead of checking their equality, it now checks their existence,...

senbaikang

move `read10xVisium` to `TENxIO`

27

relates to #114 #116 #119 #123

HelenaLC

error adding image

7

Hi, I am trying to add a high resolution image to my spe object as follows ``` spe

alfonsosaera

spatial proteomics data to SPE

1

Hi. I have data from a spatial proteomics experiment in the format shown below, which just contains x-y co-ordinates, intensity and mz values. I would like to read this into...

cathalgking

Possibility of adding `in_filtered` to read10xVisium(data = "raw")

4

Hi, We noticed an issue between reading the `raw` and `filtered` outputs from SpaceRanger that I'm not sure whether `read10xVisium()` could address or not. I incorrectly thought that the only...

lcolladotor

Problem with installing due to the dependency `magick`

5

Hi! apparently there is a new dependency `magick` added. I can not install it on my machine. the usual error: `1: In .inet_warning(msg) :installation of package ‘magick’ had non-zero exit...

EliHei2

Hi, Currently, the sanity check of `imgData` requires the `DataFrame` object to have exactly four columns `c("sample_id", "image_id", "data", "scaleFactor")`. Do you consider making it more flexible by checking instead...

senbaikang

Deprecate BumpyMatrix functionality for molecule-based data

2

We previously included some functionality using `BumpyMatrix` to store molecule-based spatial transcriptomics data, along with an example dataset from the `seqFISH` platform in the `STexampleData` package. This is now obsolete,...

lmweber