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Papatheodorou-Group / BENGAL

Nextflow pipeline for cross-species integration and assessment of single cell RNA-seq datasets
GNU General Public License v3.0
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Assessment scripts missing #1

Closed Hofphi closed 1 year ago

Hofphi commented 1 year ago

Hi,

first of all I would like to thank you for this great benchmarking pipeline!! I'd really liked to test this with my own datasets, however I have noticed that some scripts are missing to run the integration-assessment.

The following scripts are missing:

sccaf_assessment_metadata.py
sccaf_projection_multiple_species.py
kbet_multiple_species.R
scIB_metrics.py
scIB_trajectory.py

Would you be able to provide those scripts?

Furthermore, I noticed that the implementation of a SAMap integration-workflow is missing but you do report results in your preprint. Is there a reason why this implementation is missing?

Looking forward to hear from you.

Best, Philipp

YY-SONG0718 commented 1 year ago

Hi Philipp,

The scripts have been provided along with updates.

Kind regards, Yuyao