carpenter-singh-lab/2022_Haghighi_NatureMethods

Missing files for reproducing results

Opened this issue · 3 comments

alonshpigler commented

Hi,

Thanks for sharing this data along with the detailed analysis!
I'm trying to reproduce the results from the paper, and found that there are some files are missing in order to do that. These files are loaded from the following workspace: "../JDR/".

For example, in the MoA prediction notebook:

rgcca_factors_ge=pd.read_csv("../JDR/results_CP_GE_cdrpbio/factors_rgcca_ge.txt",sep="\t").reset_index(drop=True).add_suffix('_ge')

Is there a possibility to add these to the repo?

In addition, the scripts for MoA clustering will also be beneficiary if shared.

Thanks!

shntnu commented

@alonshpigler thanks for your interest in our work and for pointing us to this missing component.

It appears that this folder was never committed to the repository, and we'd need to recreate it from scratch. I don't have an ETA on that right now.

We will loop back about the MOA clustering scripts.

MarziehHaghighi commented
  • MOA clustering scrips can indeed be found here and are not part of this repository. You will need to feed this the data provided in this benchmark into these scrips to generate the results in this paper!
shihanyu commented

yes， same problem miss JDR folder. when run
rgcca_factors_cp=pd.read_csv("../JDR/results_CP_GE_lincs/factors_rgcca_cp.txt",sep="\t").reset_index(drop=True)