Nanostring-Biostats / CosMx-Analysis-Scratch-Space

This repository is an exploratory resource to accelerate opensource analysis of CosMx® Spatial Molecular Imager (SMI) data. Contained here are and writeups and vignettes addressing a variety of topics discussed when analyzing single-cell spatial data.
https://nanostring-biostats.github.io/CosMx-Analysis-Scratch-Space/
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conversion of AtoMx outputs to h5ad for squidpy and interactive viewer #52

Closed lidanwu closed 5 months ago

lidanwu commented 5 months ago

Contents in this PR:

The conversion of AtoMx exported results into .h5ad file would facilitate seamless integration into Python-based single-cell analysis workflows.

To run python code in quarto in R studio, you would need to set the reticulate package correctly. You can do that when you start a new R session fresh.

# find python for an existing env
py <- rminiconda::find_miniconda_python("nanopipeline_python")
# set to use it
reticulate::use_python(py)
# install more python package to that env
rminiconda::rminiconda_pip_install(name = "nanopipeline_python", pkg_name = c("pandas", "matplotlib", "seaborn"))
lidanwu commented 5 months ago

@crwilliams11 , I added in some more notes on FastReseg post based on our conversation in this PR. Hopefully, this is more clear now.

lidanwu commented 5 months ago

@crwilliams11 , thank you for the careful review and nice suggestions. I have incorporated them. Please take a look and let me know if needs any further edits