It is my pleasure to announce that there is now a documented way to reproduce the results in TSP_cell_cycle_analysis.ipynb in this commit of my fork of this repository.
The environment configuration in my fork has been reverse engineered because it was not published. Is there any chance a conda env export output of the original environment still exists somewhere? Or even the environment? Based on the notebook it had the name tissue and live in /Users/sabrina.richter/anaconda3/envs/tissue.
There is one inconsistency I could not resolve. It is related to the reading and subsequent use of 20210919_DIANN_SingleCellOutput.pg_matrix_cellcyclepred.tsv. The reproduction does not raise the same warnings as the original and I believe it is because the file available might be slightly different from what was used.
Thank you for the nice work and choosing to release it under a permissive license.
Hi Theis Lab,
It is my pleasure to announce that there is now a documented way to reproduce the results in
TSP_cell_cycle_analysis.ipynbin this commit of my fork of this repository.The environment configuration in my fork has been reverse engineered because it was not published. Is there any chance a
conda env exportoutput of the original environment still exists somewhere? Or even the environment? Based on the notebook it had the nametissueand live in/Users/sabrina.richter/anaconda3/envs/tissue.There is one inconsistency I could not resolve. It is related to the reading and subsequent use of
20210919_DIANN_SingleCellOutput.pg_matrix_cellcyclepred.tsv. The reproduction does not raise the same warnings as the original and I believe it is because the file available might be slightly different from what was used.Thank you for the nice work and choosing to release it under a permissive license.
With kind regards, Fabian