cytofQC-package: cytofQC: Event labeling for quality control of CyTOF data

In jillbo1000/cytofQC: Labels normalized cells for CyTOF data and assigns probabilities for each label

cytofQC: Event labeling for quality control of CyTOF data

Description

Labels observations in a CyTOF dataset as a cell, gdpZero (zero for at least one Gaussian parameter), bead, debris, doublet, or dead cell.

Details

Data from an fcs file are read directly into a SingleCellExperiment using the readCytof function.

The data can be labeled with a single function, labelQC, which can be customized. Labeling can also be done using a set of other functions that first select a set of events that clearly look like the event type being modeled and then use those events to train a statistical learning model that can identify the event type. These functions are discussed and demonstrated in the vignette.

A plotting function called cytofHist is included that makes assessing the characteristic of the data and labeling easy.

The package also includes a function called cytofQCreport that generates a report of the labeling and can generate a umap created with the QC variables and colored by event label.

Package:	cytofQC
Type:	Package
Version:	0.99.3
Date:	2022-11-11
License:	Artistic-2.0

Author(s)

Maintainer: Jill Lundell <[e-mail]>

Authors: J. Lundell, K. Street

jillbo1000/cytofQC documentation built on Aug. 23, 2023, 9:47 p.m.