Benchmarking differential abundance methods for finding condition-specific prototypical cells in multi-sample single-cell datasets.

"availability of data and materials the raw data for the covid-19 pbmc scrna-seq dataset is publicly available through the ncbi gene expression omnibus (geo; https://www ncbi nlm nih gov/geo/ ) repository with accession number gse150728 [ 31 ].; the raw data of the human pancreas scrna-seq data is publicly available at the european nucleotide archive (ena; https://www ebi ac uk/arrayexpress/experiments/ ) repository under accession number: e-mtab-5061 [ 32 ].; the raw data of the bcr-xl dataset including fcs files and their corresponding metadata and annotations can be downloaded from flowrepository with accession number fr-fcm-zyl8 [ 33 ].; the levine32 cytof dataset is available in flowrepository with accession number fr-fcm-zzph [ 34 ]. all code to reproduce results are available at https://github com/compcy-lab/benchmarkda and in the zenodo repository [ 35 ]."

"in our experiments we used the official da-seq implementation which can be accessed at https://github com/klugerlab/daseq .; we used the meld python package which can be accessed at https://github com/krishnaswamylab/meld .; the cna approach is implemented in python and is available at https://github com/immunogenomics/cna .; all code to reproduce results are available at https://github com/compcy-lab/benchmarkda and in the zenodo repository [ 35 ].; source code is released under the mit license."

"Declarations Ethics approval and consent to participateNot applicable. Consent for publicationAll authors consent to the publication. Competing interestsThe authors declare that they have no competing interests. Competing interests The authors declare that they have no competing interests."

"Funding This work is supported by The National Institutes of Allergy and Infectious Diseases of the National Institutes of Health under the award number 1R21AI171745-01A1 (NS). We also acknowledge support from the National Institute of General Medical Science of the National Institutes of Health under the award 5T32 GM067553 (AP)."