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Dear professor:
The work here is highly valuable. I want to replicate the workflow according to the examples, but I can't find several important files. They are "./data/molecular-atlas-master/data/sl…
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Dear Professor,
Thanks for your explanation and patience! I want to know how can I find the DLPFC dataset in the tutorial:
anno_df = pd.read_csv('./data/spatialLIBD/barcode_level_layer_map.tsv',…
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Hello, can you provide the data for analysis in visium_human_dorsolateral_prefrontal_Cortex.r?
I can get the raw data, but I'm not sure what goes from the raw data to the data for your analysis.
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Maybe this is already possible? But I have 6 10x Visium datasets that I would like to upload to 1 shiny app for data mining and sharing. If possible, would the best approach be to construct 1 master S…
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Right now `spatialLIBD` is built upon the `SpatialExperiment` container class. There is also https://bioconductor.org/packages/SpatialFeatureExperiment/ that can support non-Visium spatially-resolved …
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Can iSEE support Spatial transcriptomics data that is contained within a SPE (SpatialExperiment) object? I have 10x Visium data in an SPE and tried running ```iSEE(SPE)``` which opened a shiny app wit…
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I am using the example data in the documentation and I am not able to run the app locally. I am getting the following error when i use run_app() or any interactive website visualisation as mentioned …
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Hi,
It is a fantastic method for analyzing spatial transcriptomics!
I tried to cluster DLPFC samples with SCGDL following the tutorial you present. I found the outcomes are quite different from …
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Thank you for providing such excellent work. As we would like to use the model for some analytical tasks, could you please provide parameters for other sliced models? We appreciate your help very much…
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I recently ran registration_wrapper() on a very high-dimension dataset (~80 or ~200 clusters across 47 samples, depending on the granularity) and twice had runs go >8 hours before seeing warnings abou…