Microscopy Based Cytometry Data Analysis Package


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Documentation for package ‘Rcell’ version 1.2-0

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A C E G I L M O P Q R S T U V W X Y Z misc

Rcell-package Microscopy Based Cytometry Data Analysis Package

-- A --

ACL394 Time Dependent Dose Response of Yeast Cells to Mating Pheromone
ACL394filtered Time Dependent Dose Response of Yeast Cells to Mating Pheromone
add.maj.min.axis Transform Cell Image
add.nucleus.boundary Transform Cell Image
aggregate.cell.data Compute Summary Statistics of Cell Data Subsets
append.anular.c Append Variables
append.anular.r Append Variables
append.anular.y Append Variables
append.in.focus Append Variables
append.memRec.r Append Variables
append.memRec.y Append Variables
append.oif.interval Append Variables from OIF files
append.oif.time Append Variables from OIF files
append.z.scan Append Variables
as.cell.data Coerce to Cell Data
as.cell.data.list Coerce to Cell Data
as.data.frame.cell.data Coerce to a Data Frame

-- C --

cardinality.plot Map Cell Counter Tags to Cells
caxis Zoom in a ggplot Object
cdata Coerce to a Data Frame
cell.counter Map Cell Counter Tags to Cells
cell.data Cell Data Object
cell.hclust Hierarchical Clustering of Cell Data
cell.image Get Cells Images
chclust Hierarchical Clustering of Cell Data
ciciply Transform Cell Image
cimage Images Layout
cimage.cell.data Images Layout
cimage.cell.image Images Layout
cimage.default Images Layout
clayer Plotting Cell Data Objects
clayermean Plotting Cell Data Objects
clayermeans Plotting Cell Data Objects
clayermedian Plotting Cell Data Objects
cnormalize Transform Cell Image
cplot Plotting Cell Data Objects
cplotmean Plotting Cell Data Objects
cplotmeans Plotting Cell Data Objects
cplotmedian Plotting Cell Data Objects
creshape Reshape a Cell Data Object

-- E --

Extract.cell.data Coerce to a Data Frame

-- G --

get.cell.image Get Cells Images
get.cell.image.cell.data Get Cells Images
get.cell.image.data.frame Get Cells Images
get.cell.image.default Get Cells Images
ggplot.theme ggplot2 themes
ggplot.themes ggplot2 themes
ggplot2.theme ggplot2 themes
ggplot2.themes ggplot2 themes

-- I --

img.desc Get Cells Images
is.cell.data Coerce to Cell Data
is.cell.image Get Cells Images

-- L --

load.cell.data Load Cell-ID Data
load.cellID.data Load Cell-ID Data
load.pdata Merge a Data Frame to a Cell Data Object

-- M --

map.cells.points Map Cell Counter Tags to Cells
merge.cell.data Merge a Data Frame to a Cell Data Object
misc Miscellaneous Functions

-- O --

OIF Append Variables from OIF files

-- P --

paste_data_error Miscellaneous Functions
paste_EC50_n Miscellaneous Functions
paste_intercept_slope Miscellaneous Functions
paste_parameter Miscellaneous Functions
pdata Time Dependent Dose Response of Yeast Cells to Mating Pheromone
plot.cell.data Plotting Cell Data Objects
plot.Image Plot Image
pos1.cell.counter Time Dependent Dose Response of Yeast Cells to Mating Pheromone
print.cell.image Get Cells Images
print.summary.cell.image Get Cells Images

-- Q --

QC.execute Quality Control Filter
QC.filter Quality Control Filter
QC.reset Quality Control Filter
QC.undo Quality Control Filter

-- R --

Rcell Microscopy Based Cytometry Data Analysis Package
remove.vars Subset a Cell Data Objects
reshape Reshape a Cell Data Object
reshape.cell.data Reshape a Cell Data Object

-- S --

select.cells Select Subset of Cells
select.vars Select Variables
show.image Show a Image
show.img Show a Image
StatBootstrap Calculate bootstraps confidence intervals of a time course
StatInteractionError Calculate summary statistic after correcting for the 'sample effect'.
StatSummaryGroup Summarise y and x values according to user defined groups.
stat_bootstrap Calculate bootstraps confidence intervals of a time course
stat_interactionError Calculate summary statistic after correcting for the 'sample effect'.
stat_summaryGroup Summarise y and x values according to user defined groups.
subset.cell.data Subset a Cell Data Objects
summary.cell.data Cell Data Object Summary
summary.cell.image Get Cells Images

-- T --

theme_black ggplot2 themes
theme_complete_bw ggplot2 themes
theme_fullframe ggplot2 themes
theme_invisible ggplot2 themes
theme_minimal ggplot2 themes
theme_minimal_cb ggplot2 themes
theme_minimal_cb_L ggplot2 themes
theme_minimal_light ggplot2 themes
transform.by Transform a Cell Data Object
transform.by.cell.data Transform a Cell Data Object
transform.by.data.frame Transform a Cell Data Object
transform.by.default Transform a Cell Data Object
transform.cell.data Transform a Cell Data Object
transformBy Transform a Cell Data Object
transformBy.cell.data Transform a Cell Data Object
transformBy.data.frame Transform a Cell Data Object
transformBy.default Transform a Cell Data Object

-- U --

update.n.tot Calculate Total Number of Frames for Each Cell
update_img.path Update Image Path
update_n.tot Calculate Total Number of Frames for Each Cell

-- V --

vplayout Miscellaneous Functions

-- W --

with.cell.data Evaluates an Expression in a Cell Data Object.

-- X --

X Time Dependent Dose Response of Yeast Cells to Mating Pheromone
xzoom Zoom in a ggplot Object

-- Y --

yzoom Zoom in a ggplot Object

-- Z --

zoom Zoom in a ggplot Object

-- misc --

[.cell.data Subset a Cell Data Objects
[[.cell.data Coerce to a Data Frame