flowQB: Automated Quadratic Characterization of Flow Cytometer Instrument Sensitivity: Q, B and CV instrinsic calculations
Version 2.4.0

flowQB is a fully automated R Bioconductor package to calculate automatically the detector efficiency (Q), optical background (B) and intrinsic CV of the beads.

Browse man pages Browse package API and functions Browse package files

AuthorJosef Spidlen, Faysal El Khettabi, Wayne Moore, David Parks, Ryan Brinkman
Bioconductor views FlowCytometry MultiChannel OneChannel PeakDetection QualityControl Regression
Date of publicationNone
MaintainerJosef Spidlen <jspidlen@gmail.com>
LicenseArtistic-2.0
Version2.4.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("flowQB")

Man pages

calc_mean_sd_197: Calculate the mean and the standard deviation of Standford's...
calc_mean_sd_background: Calculate the mean and the standard deviation.
calc_mean_sd_capture: Calculate the mean and the standard deviation for the stained...
calc_mean_sd_capture_all: Calculate the mean and the standard deviation for the stained...
calc_mean_sd_duke: Calculate the mean and the standard deviation of calibration...
find_peak: Find density peak in the provided vector of values
fit_beads: Fit multi-level bead data.
fit_led: Fit LED data.
fitted_ellipse_gate: Fit and apply an ellipse gate
get_results_for_dyes: Extract dye results from a data frame with detector results.
peak_gate-methods: Gate a 1D density peak in the provided object
pick_parameters-methods: Pick channel names
qb_from_fits: Extract Q, B and the intrinsic CV0 from fitting results
split_in_two-methods: Split an object in a low density region

Functions

calc_mean_sd_197 Man page Source code
calc_mean_sd_background Man page Source code
calc_mean_sd_capture Man page Source code
calc_mean_sd_capture_all Man page Source code
calc_mean_sd_duke Man page Source code
censor_peak_statistics Source code
find_peak Man page Source code
fit_beads Man page Source code
fit_led Man page Source code
fit_spherotech Man page Source code
fit_thermo_fisher Man page Source code
fitted_ellipse_gate Man page
fitted_ellipse_gate,flowFrame,ANY-method Man page
fitted_ellipse_gate,flowFrame,fitted_ellipse_gate-method Man page
fitted_ellipse_gate,flowFrame-method Man page
get_peak_statistics Source code
get_results_for_dyes Man page Source code
peak_gate Man page
peak_gate,flowFrame,ANY-method Man page
peak_gate,flowFrame,peak_gate-method Man page
peak_gate,flowFrame-method Man page
peak_gate,matrix,ANY-method Man page
peak_gate,matrix,peak_gate-method Man page
peak_gate,matrix-method Man page
pick_parameters Man page
pick_parameters,flowFrame,ANY-method Man page
pick_parameters,flowFrame,pick_parameters-method Man page
pick_parameters,flowFrame-method Man page
qb_from_fits Man page Source code
split_in_two Man page
split_in_two,flowFrame,ANY-method Man page
split_in_two,flowFrame,split_in_two-method Man page
split_in_two,flowFrame-method Man page
split_in_two,matrix,ANY-method Man page
split_in_two,matrix,split_in_two-method Man page
split_in_two,matrix-method Man page
usable_rows Source code

Files

DESCRIPTION
NAMESPACE
R
R/calc_mean_sd_functions.R
R/fit_functions.R
R/fitted_ellipse_gate.R
R/helper_functions.R
R/peak_gate.R
R/pick_parameters.R
R/split_in_two.R
build
build/vignette.rds
inst
inst/NEWS
inst/doc
inst/doc/flowQBVignettes.R
inst/doc/flowQBVignettes.Rnw
inst/doc/flowQBVignettes.pdf
inst/extdata
inst/extdata/readme.txt
inst/unitTests
inst/unitTests/test_calc_mean_sd_197.R
inst/unitTests/test_calc_mean_sd_background.R
inst/unitTests/test_calc_mean_sd_capture.R
inst/unitTests/test_calc_mean_sd_duke.R
inst/unitTests/test_find_peak.R
inst/unitTests/test_fit_beads.R
inst/unitTests/test_fit_led.R
inst/unitTests/test_fitted_ellipse_gate.R
inst/unitTests/test_helpers.R
inst/unitTests/test_peak_gate.R
inst/unitTests/test_pick_parameters.R
inst/unitTests/test_split_in_two.R
man
man/calc_mean_sd_197.Rd
man/calc_mean_sd_background.Rd
man/calc_mean_sd_capture.Rd
man/calc_mean_sd_capture_all.Rd
man/calc_mean_sd_duke.Rd
man/find_peak.Rd
man/fit_beads.Rd
man/fit_led.Rd
man/fitted_ellipse_gate.Rd
man/get_results_for_dyes.Rd
man/peak_gate-methods.Rd
man/pick_parameters-methods.Rd
man/qb_from_fits.Rd
man/split_in_two-methods.Rd
tests
tests/runTests.R
vignettes
vignettes/Refs.bib
vignettes/flowQBVignettes.Rnw
vignettes/kmeans.png
flowQB documentation built on May 20, 2017, 10:07 p.m.