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Bioinformatics-Service-MPI-Munster / stewen-2024-nat-comms

Code for the study "Eph-ephrin signaling couples endothelial cell sorting and arterial specification" by Stewen J, Kruse K, Godoi-Filip AT, Jeong H, Adams S, Berkenfeld F, Stehling M, Red-Horse K, Adams RH, Pitulescu ME
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script #1

Open BDXH-FY24 opened 3 months ago

BDXH-FY24 commented 3 months ago

Hi Stewen,

Can you share the script for rhapsody-demultiplex and rhapsody-extract-barcode?

kaukrise commented 3 months ago

They are available as part of a more general Python module: https://github.com/Bioinformatics-Service-MPI-Munster/scrna-tools

You can install it with pip.

BDXH-FY24 commented 3 months ago

pip install scrna-tools?

kaukrise commented 3 months ago

No, it is not available on Pypi, you will have to git clone the repository first and then install from there. Here are the basic steps:

git clone https://github.com/Bioinformatics-Service-MPI-Munster/anndataview
git clone https://github.com/Bioinformatics-Service-MPI-Munster/scrna-tools

And then install with pip:

pip install ./anndataview
pip install ./scrna-tools

I've added these instructions to the README, too.

BDXH-FY24 commented 3 months ago

Thanks, that works.

BDXH-FY24 commented 3 months ago

one more ask, could you please share the file: rhapsody_whitelist.txt

kaukrise commented 3 months ago

You can find it here, at the bottom of the page: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE223738

BDXH-FY24 commented 3 months ago

cool, thank you so much!

BDXH-FY24 commented 3 months ago

One more question, the beads for Rhapsody is enhance V2?

kaukrise commented 3 months ago

No, these are V1

BDXH-FY24 commented 3 months ago

Thanks a lot