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Build `SpatialExperiment` object containing data from all samples (all 3 rounds) in a single object:
Notes:
- include metadata column for round IDs
- add VistoSeg outputs from `count_spots.csv` f…
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Based on a discussion with @jashapiro in slack, before doing #63, we should decide if we would like to create `rds` files for the spatial libraries for users, or if we would prefer to create a `tar.gz…
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/Nanostring-Biostats/NanoStringExperiment
Confirm …
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In the `read10xVisium()` source code, the `.read_xyz()` function to read the `tissue_positions_list.csv` file reads the position data columns in order as `pxl_col`, `pxl_row`:
https://github.com/drig…
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/vitessce/vitessceR
Confirm the following by editi…
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/MarcElosua/SPOTlight
Confirm the following by edi…
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Hi,
Very useful software!
I just wonder how to use it with the 10 x visium spaceranger output?
Do you have a brief intro for that?
Thank you.
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https://mp.weixin.qq.com/s/zj9qeZah50ZWLa0GbUCMpw
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Hi,
I would like to do a neighbourhood analysis, but I am having some issues with the input files.
I have done some clustering with FlowJo (using the fcs files exported with Histocat). But I have …
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Because we have a project that has spatial transcriptomics data, we will need to add a workflow to process the spatial transcriptomics data. Alevin-fry does provide a [tutorial on how to use Alevin-fr…