cyCombine allows for robust integration of single-cell cytometry datasets within and across technologies

Profiling the phenotypes of the non-malignant immune cells from peripheral blood mononuclear cell samples from 20 healthy donors and samples from 56 patients with CLL, which were sampled at two distinct time points (T1 and T2). Samples were B cell-depleted. The data was used to validate the cyCombine batch correction tool.
Notes:
The samples were processed with two panels and in seven batches per panel. Some samples were excluded during experimental processing. Raw FCS files were normalized using bead standards, compensated, deconvoluted, and pre-gated to live intact singlet cells. The cyCombine R package is available on GitHub (https://github.com/biosurf/cyCombine).