Normalize & Denoise Droplet Single Cell Protein Data (CITE-Seq)

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Documentation for package ‘dsb’ version 1.0.3

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cells_citeseq_mtx small example CITE-seq protein dataset for 87 surface protein in 2872 cells
DSBNormalizeProtein DSBNormalizeProtein R function: Normalize single cell antibody derived tag (ADT) protein data. This function implements both step I (ambient protein background correction) and step II. (defining and removing cell to cell technical variation) of the dsb normalization method. See <https://www.biorxiv.org/content/10.1101/2020.02.24.963603v3> for details of the algorithm.
empty_drop_citeseq_mtx small example CITE-seq protein dataset for 87 surface protein in 8005 empty droplets
ModelNegativeADTnorm ModelNegativeADTnorm R function: Normalize single cell antibody derived tag (ADT) protein data. This function defines the background level for each protein by fitting a 2 component Gaussian mixture after log transformation. Empty Droplet ADT counts are not supplied. The fitted background mean of each protein across all cells is subtracted from the log transformed counts. Note this is distinct from and unrelated to the 2 component mixture used in the second step of 'DSBNormalizeProtein' which is fitted to all proteins of each cell. After this background correction step, 'ModelNegativeADTnorm' then models and removes technical cell to cell variations using the same step II procedure as in the DSBNormalizeProtein function using identical function arguments. This is a experimental function that performs well in testing and is motivated by our observation in Supplementary Fig 1 in the dsb paper showing that the fitted background mean was concordant with the mean of ambient ADTs in both empty droplets and unstained control cells. We recommend using 'ModelNegativeADTnorm' if empty droplets are not available. See <https://www.biorxiv.org/content/10.1101/2020.02.24.963603v3> for details of the algorithm.