lieberinstitute / humanpilot Goto Github PK

Dear spatialLIBD team,
I have completed the installation of spatialLIBD, but when executing spe <- fetch_data(type = "spe"), an error occurred. The error message is as follows:

I would like to understand the cause of this error.

There are quality problems with pathology images, and noise that should not be present can be seen when the original image is enlarged. Are there no high quality pathology images available for download? Or ISH images.

The layer guess file for samples 151507 and 151669

contain multiple samples.

can you take the genes in the previous layer marker table, and make a boxplot of mean expression in brainseq phase2 DLPFC, within fetal and then adult? ie 4 boxes: fetal:layerMarker, fetal:notLayerMarker, adult:layerMarker, adult:nonLayerMarker (where there are way more points in the nonLayerMarker boxes)

In Lukas' code he refers to column 5 of that table as the columns and column 6 as the rows whereas your code does the reverse.

We need to decide which is correct.

Dear spatialLIBD team,

Thanks for sharing the awesome resources.

I'd like to download the fastq/bam files from http://research.libd.org/globus/

I log in to the platform but the download button is gray.

Then, I click on Transfer or Sync to ... and the start button but it still doesn't work. Do I miss anything? Any comments are highly appreciated:)

Hello, I am currently exploring the dataset for a project that I am doing but I can't seem to find a comprehensive documentation on the available data. I am specifically looking for the ground truth but I am not quite sure if I can use layer_guess.

Any help would be appreciated.

Thanks!

Hello! Thank you for your great work on this package. I found it very easy to use and your documentation is excellent. I have a question regarding the data availability from your paper.
In your paper (Maynard et al 2021 Nat. Neurosci), you spatially registered three independent snRNA-seq datasets, and one of these datasets was generated by your research team. I am wondering whether this annotated snRNA-seq dataset is publicly available. (From my understanding, the raw data provided at the Globus link is Visium data only, and the data which is available for download through the spatialLIBD package is also Visium-based.) Please let me know if there is any way I can access this data. Thank you!

Hello,

I was wondering if it was possible to also upload aligned_fiducials.jpg, scalefactors_json.json, and tissue_positions_list.csv from the spatial output in cellranger output?

Thanks,
Chang