ktest_experiment_genome_biology_2024

Use this code to reproduce the analyses of the Ozier-Lafontaine et al. 2024 Genome Biology paper "ktest : Kernel-Based Testing for Single-Cell Differential Analysis"

## Data availability

• The reversion and scChIP-Seq datasets can be loaded here : https://zenodo.org/records/11001869
• The experimental scRNAseq datasets associated to Squair, J.W., Gautier, M., Kathe, C. et al. Confronting false discoveries in single-cell differential expression. Nat Commun 12, 5692 (2021) can be loaded here : https://zenodo.org/records/5048449

## Folders

• simulated_data/ analyses corresponding to Section 2.4 "Kernel testing is calibrated and powerful on simulated data"
• experimental_scrnaseq_data/ analyses corresponding to Section 2.5 "Challenging DEA metods on experimental scRNA-Seq data"
• reversion/ analyses corresponding to Section 2.6 "Kernel testing reveals the heterogeneity of reverting cells"
• scchipseq/ analyses corresponding to Section 3 "Towards a new testing framework for differential binding analysis in single-cell ChIP-Seq data"

## ktest versions

The analyses are performed with different versions of the ktest package.

• For scripts in simulated_data/ and experimental_scrnaseq_data/ :

pip  install ktest@git+https://github.com/LMJL-Alea/ktest@publication_genome_biology#subdirectory=python

• For scipts in reversion/ and scchipseq/ :

pip  install ktest@git+https://github.com/LMJL-Alea/ktest@publication_genome_biology_reversion#subdirectory=python