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KrishnaswamyLab / MELD

Quantifying experimental perturbations at single cell resolution
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Tutorial for running MELD on >2 treatment conditions #46

Open mdmanurung opened 3 years ago

mdmanurung commented 3 years ago

Dear Daniel,

When would you release the tutorial for analysing > 2 groups using MELD?

Thanks in advance!

Mikhael

dburkhardt commented 3 years ago

Hi @MikhaelManurung , thanks for your interest in MELD! I'm actively working to get v1.0.0 onto pypi which has better support for >2 conditional categories. I would prefer to have a publicly available dataset with multiple conditions, do you have one in mind? Otherwise I was just going to use the replicate labels from the zebrafish dataset.

mdmanurung commented 3 years ago

Hi @dburkhardt, how about the data set that was used for the SAUCIE paper? I think there were 3 groups, right?

dburkhardt commented 3 years ago

@MikhaelManurung, I talked with @mattamodio and the datasets used in SAUCIE had significant batch effects between samples that needed to be corrected prior to analysis. I'm hesitant to create a tutorial using a dataset that requires such strong batch normalization prior to analysis.

One idea is to repeat the analysis for the donors as was done in the current version of the manuscript on BioRxiv. It's not quite three different experimental treatment conditions, but the overall process would be similar.

I'm open to other suggestions too!

yuGithuuub commented 3 years ago

Hi Daniel, When will the tutorial on using MELD analysis> 2 groups be released? Very much looking forward to its appearance Thanks ! ^-^

zyll123 commented 5 months ago

Sorry, I'm not sure if I miss anything. So where can I find the tutorial for >3 conditions now ?