i.score

A data frame containing gene counts for cells.

object

Choose from "raw.data" or "main.data", "imputed.data", default = "main.data".

data.type

Genes that are used as a marker for phases.

scoring.List

Return the data or object. If FALSE the object would be returned.

return.stats

Choose from "sum","mean" or "tirosh" for scoring method. See: https://science.sciencemag.org/content/352/6282/189

scoring.method

This function takes an object of class iCellR and assignes cell cycle stage for the cells.

A toolkit that allows scientists to work with data from single cell sequencing technologies such as scRNA-seq, scVDJ-seq and CITE-Seq. Single (i) Cell R package ('iCellR') provides unprecedented flexibility at every step of the analysis pipeline, including normalization, clustering, dimensionality reduction, imputation, visualization, and so on. Users can design both unsupervised and supervised models to best suit their research. In addition, the toolkit provides 2D and 3D interactive visualizations, differential expression analysis, filters based on cells, genes and clusters, data merging, normalizing for dropouts, data imputation methods, correcting for batch differences, pathway analysis, tools to find marker genes for clusters and conditions, predict cell types and pseudotime analysis. See Khodadadi-Jamayran, et al (2020) <doi:10.1101/2020.05.05.078550> and Khodadadi-Jamayran, et al (2020) <doi:10.1101/2020.03.31.019109> for more details.

i.score: Cell cycle phase prediction

Description

Usage

Arguments

Value