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Dawnn benchmarking dataset: Keratinocytes processing and label simulation

dataset
posted on 2023-05-04, 16:09 authored by George HallGeorge Hall, Sergi Castellano HerezaSergi Castellano Hereza

This project is a collection of files to allow users to reproduce the model development and benchmarking in "Dawnn: single-cell differential abundance with neural networks" (Hall and Castellano, under review). Dawnn is a tool for detecting differential abundance in single-cell RNAseq datasets. It is available as an R package here. Please contact us if you are unable to reproduce any of the analysis in our paper.

The files in this collection correspond to the benchmarking dataset based on single-cell RNAseq of keratinocytes.


FILES:

Input data

Dataset from "Short-Term Treatment with Rho-Associated Kinase Inhibitor Preserves Keratinocyte Stem Cell Characteristics In Vitro". Cells 12(3), 346 (2023).

  • skin_data_end_pipeline_1458110522.rds RDS object file to load dataset.

Data processing code

  • simulate_skin_labels_Rscript.R R code to simulate labels for benchmarking.
  • simulate_skin_labels_bash.sh Bash script to execute simulate_skin_labels_Rscript.R. Outputs stored in benchmark_dataset_skin.csv.

Resulting datasets

  • benchmark_dataset_skin.csv Cell labels generated by simulate_skin_labels_bash.sh.

Funding

NIHR Great Ormond Street Hospital Biomedical Research Centre

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