search

PayamDiba / SERGIO

A simulator for single-cell expression data guided by gene regulatory networks
GNU General Public License v3.0
55 stars 28 forks source link

600 Gene, 6 Cell Types Dataset? #12

Open aradley opened 3 years ago

aradley commented 3 years ago

Hi,

Hope you're well.

I was wondering if you could help me generate the inputs for a 600 gene, 6 cell types dynamic expression dataset please? Or something similar. The closest dataset inputs that you have provided are DS3 with 1200 genes and 9 cell types. Unfortunately when running the dynamic version of SERGIOI run into two issues. Firstly I have to put the number of cells per cell type to less than 100 cells, otherwise I encounter a memory issue and python shuts down. This then leads to me having to re-run the software many times to try and get enough cells. However, because the run time is so long, it is then not practical for parameter tuning to get smooth cell type transitions.

I'm hoping a 600 gene, 6 cell type dataset will overcome these problems. If you have other suggestions though I'd be happy to hear them.

Best,

Arthur

aradley commented 3 years ago

Hi,

Sorry to pester, but if you have time it would really help me validate and write up my software if I could get this working.

Best,

Arthur

PayamDiba commented 3 years ago

I can help you simulate the data as I have access to a cluster with multiple computational nodes on which I can parallelize the simulations. Please contact me by Email and tell me about the differentiation trajectory and GRN structure you want to simulate.

aradley commented 3 years ago

This sounds great thank you very much!

May I have your email address please?