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yanailab / PanCancer

Data available at: https://www.dropbox.com/sh/jh4s57kgbb0rnxe/AABoMK466cGc1OKsOuFN10wca?dl=0 and https://nyulangone-my.sharepoint.com/:f:/g/personal/dalia_barkley_nyulangone_org/EuHetdAOc2pLjm9XUwqdWicBnlXIbyvHx-EOC-inP-SGUg?e=rxa7Ry
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module data #4

Open Peiyao-Z opened 1 year ago

Peiyao-Z commented 1 year ago

Hi! I found your finding very interesting. I wonder if you can provide modules.RData for modules. I was trying to go over the whole process to get the cell state values. Thank you! Peiyao

jpark27 commented 1 year ago

Dear Yanai Lab,

Hi, all! Salut you all with publication of recent N.Genetics paper and really enjoyed reading it :-)

[1] We are also quite interested in reproducing results from the paper using your scripts and subsequently apply in-house dataset. As Peiyao-Z mentioned earlier, do you think one can upload .RData that are loaded on each script but not available atm?

e.g.,) Finding.R -> parameters.RData [8] -> res.malignant.RData [15] -> srt.malignant.RData [21] -> regulons.malignant.RData [508]

experiments.R
-> srt.RData [41] -> conv.RData [231] -> modules.RData [239] -> colors.module.RData [246] -> modules.Mm.RData [249] -> Adaptive.malignant.RData [674]

[2] Also, I noticed on Part1.sh shell script, there has been mentioned about running STARCH tool but haven't seen on actual paper other than infercnv regarding CNV calling. (run_STARCH.py). Do you mind clarify on this?

[3] Lastly, as I am not avid R user, maybe can you briefly share how Yanai team run each script in order would be really useful for general public

Kudos! Jun