Single-cell-RNA-sequencing-data-analysis

R code for the analysis of single-cell RNA sequencing analysis of human bone marrow natural killer cells as published in Frontiers in Immunology. In addition a script can be found to analyze publically available data on human circulating NK cells (~50.000 cells).

Frontiers publication

Datasets

Melsen: GSE199411

Crinier: GSE159624

Yang: GSE130430

Reproduction of figures

Quality control Melsen dataset

Clustering of Melsen dataset

Subclustering of CD56dimGZMK- population Melsen dataset

Integration Yang dataset

Integration Crinier dataset

Integration Melsen, Crinier and Yang dataset

Integration Melsen and HCA

Pseudotime analysis Melsen dataset

Sce objects

Click here to open the sce objects, as generated in the paper (big integrated objects were excluded). The objects with 'sce' in title, refer to the Melsen dataset

NK atlas peripheral blood

Datasets

Crinier et al, 2018 GSE119562

Yang et al, 2021 GSE130430

Witkowski et al, 2021 GSE184329

Ruckert et al, 2022 GSE197037