Learn R Programming

CytobankAPIstats (version 2.0)

Computes Signaling and Population Stats for Cytometry Data on Cytobank using 'CytobankAPI'

Description

Tools to process cytometry data from Cytobank into easily usable form for analysis of populations, markers, and signaling using the 'CytobankAPI' package. Learn more about Cytobank at . For more information about types of cytometry data that can be analyzed, please see: Bendall, S. C., Simonds, E. F., Qiu, P., Amir, E. D., Krutzik, P. O., Finck, R.,... Nolan, G. P. (2011) and Adan, A., Alizada, G., Kiraz, Y., Baran, Y., Nalbant, A. (2017). .

Copy Link

Version

Install

install.packages('CytobankAPIstats')

Monthly Downloads

16

Version

2.0

License

Artistic-2.0

Maintainer

Allison Throm

Last Published

June 27th, 2018

Functions in CytobankAPIstats (2.0)

Computes the arcsinh ratio of a matrix in relation to the specified column

Filters a list of fcs files by search terms

Filters matrix based on single sample name condition

Calculates percentages of of cell types of interest out of total cell population

Gets appropriate marker IDs for channels of interest

Returns a matrix of event counts or raw medians, as specified by inputs. Columns correspond to fcs files and rows to markers in cell types

Rearranges signaling results matrix with rows in the desired order as outputs

CytobankAPIstatsGUI

Exports processed events and signaling data

Filters matrix columns based on two conditions per file, e.g. patient status, stimluation, time points, etc.

Gets fcs ID numbers and sample names from a given experiment

Modifies the list obtained from a call to statistics.events to a matrix with rows corresponding to fcs files and columns corresponding to the population types

Takes the results of a call to statistics.general and returns a matrix of raw means with columns corresponding to fcs files and rows to molecules of interest in different cell types

Gets appropriate gate set IDs for populations of interest

Calculates the percentage of cell populations given an experiment

Computes the untransformed medians for cellular markers in populations of interest

Takes the results of a call to statistics.general and returns a matrix of raw medians with columns corresponding to fcs files and rows to molecules of interest in different cell types