Cleans and Normalizes FLUOstar DBF and DAT Files from 'Liposome' Flux Assays


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Documentation for package ‘normfluodbf’ version 2.0.0

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A C D E F G H I L M N O P Q R S T U V X Y misc

-- A --

add_package_namespace Add Package Namespace
analyze Analyze
analyze_ready Analyze
analyze_ready.1536well_plate_t1 Analyze
analyze_ready.1536well_plate_t2 Analyze
analyze_ready.384well_plate Analyze
analyze_ready.96well_plate Analyze
analyze_ready.default Analyze
average_fluorescence_by_row_cycle Capitalize

-- C --

capitalize Capitalize
check_broken_packages Check Broken Packages
check_dirt Check Dirt
check_package_usage Check package or function Usage
check_step Steps Utils
childtype Child Type
child_plate_type Child Type
child_plate_type.default Child Type
child_plate_type.normfluodbf_plate Child Type
clean_commas DAT file data frame cleaner.
clean_even_dat DAT file wrangler.
clean_odddat_optimus DAT file wrangler.
comma_cleaner Comma Cleaner function.
comment_out_lines Comment Out

-- D --

dat_1 dat_1.
dat_2 dat_2.
dat_3 dat_3.
dat_4 dat_4.
dat_5 dat_5.
dat_6 dat_6.
dat_7 dat_7.
dat_col_names_horizontal Attribute(s) naming function.
dat_col_names_optimus Attribute(s) naming function.
dat_col_names_prime Attribute(s) naming function.
dat_col_names_rigid Attribute(s) naming function.
decimal_scaling Normalizing Agents
decimal_scaling_df Normalizing Agents
defineparams Define Plate Parameters
definestatus Define Plate Status
definesteps Define Plate Steps
define_params Define Plate Parameters
define_params.1536well_plate_t1 Define Plate Parameters
define_params.1536well_plate_t2 Define Plate Parameters
define_params.384well_plate Define Plate Parameters
define_params.96well_plate Define Plate Parameters
define_params.default Define Plate Parameters
define_status Define Plate Status
define_status.1536well_plate_t1 Define Plate Status
define_status.1536well_plate_t2 Define Plate Status
define_status.384well_plate Define Plate Status
define_status.96well_plate Define Plate Status
define_status.default Define Plate Status
define_steps Define Plate Steps
define_steps.1536well_plate_t1 Define Plate Steps
define_steps.1536well_plate_t2 Define Plate Steps
define_steps.384well_plate Define Plate Steps
define_steps.96well_plate Define Plate Steps
define_steps.default Define Plate Steps
define_steps.normfluodbf_plate Define Plate Steps
demo Run the shiny App In addition to the functions provided in this package, the 'normfluodbf' package also provides an interactive tool that can be used to analyze liposome flux assay data more easily. The tool will be launched in a web browser.
detectoutliers Detect Outliers
detect_outliers_cn Detect Outliers
detect_outliers_time_cn Detect Outliers
dirty Status
dirty<- Status
dirutils Directory Utils

-- E --

empty_plate Plate

-- F --

find_known_liposome_dat_file Directory Utils
find_known_liposome_dbf_file Directory Utils
formatplatedata Format Plate Data
format_plate_data Format Plate Data
format_plate_data.1536well_plate_t1 Format Plate Data
format_plate_data.1536well_plate_t2 Format Plate Data
format_plate_data.384well_plate Format Plate Data
format_plate_data.96well_plate Format Plate Data
format_plate_data.default Format Plate Data

-- G --

getfilename Get File Name(s)
get_common_dat_names Get File Name(s)
get_dat_common_name Get File Name(s)
get_dat_file_name Get File Name(s)
get_dbf_file_name Get File Name(s)
get_status_value Define Plate Status
get_step_key_by_index Steps Utils
get_wells_used Wells Used
globalcache Globals Cache

-- H --

has_step Steps Utils

-- I --

init_plate Plate
isnormalized Is Normalized
is_dir Directory Utils
is_file Directory Utils
is_normalized Is Normalized
is_plate_dirty Status

-- L --

launch Run the shiny App checking dependencies in R code ... WARNING In addition to the functions provided in this package, the 'normfluodbf' package also provides an interactive tool that can be used to analyze liposome flux assay data more easily. The tool will be launched in a web browser.
liposomes_214 liposomes_214.
liposomes_215 liposomes_215.
liposomes_216 liposomes_216.
liposomes_218 liposomes_218.
liposomes_221 liposomes_221.
liposomes_227 liposomes_227.
liposome_fluor_dbfs Cleans and Normalizes DBF files obtained from experiments using the FLUOstar Omega microplate reader (from BMG LABTECH).
list_dats Directory Utils
list_dbfs Directory Utils
loadplatedata Load Plate Data
loadplatemeta Load Plate Meta
load_plate_data Load Plate Data
load_plate_data<- Load Plate Data
load_plate_meta Load Plate Meta
load_plate_meta<- Load Plate Meta
load_rds_plate Save and Load Plate
log_transformation Normalizing Agents

-- M --

min_max_norm Normalizing Agents
min_max_norm_df Normalizing Agents
min_max_norm_percent Normalizing Agents
min_max_norm_percent_df Normalizing Agents
modifyplatedata Modify Plate Data
modify_plate_data Modify Plate Data
modify_plate_data.1536well_plate_t1 Modify Plate Data
modify_plate_data.1536well_plate_t2 Modify Plate Data
modify_plate_data.384well_plate Modify Plate Data
modify_plate_data.96well_plate Modify Plate Data
modify_plate_data.default Modify Plate Data
move_file Move File
multiplot Multiplot

-- N --

name Plate Name
name<- Plate Name
new_plate Plate
next_step Steps Pipeline
normalize Normalize
normalize.1536well_plate_t1 Normalize
normalize.1536well_plate_t2 Normalize
normalize.384well_plate Normalize
normalize.96well_plate Normalize
normalize.default Normalize
normalizebywell Normalize by Well
normalize_by_well Normalize by Well
normalize_by_well.1536well_plate_t1 Normalize by Well
normalize_by_well.1536well_plate_t2 Normalize by Well
normalize_by_well.384well_plate Normalize by Well
normalize_by_well.96well_plate Normalize by Well
normalize_by_well.default Normalize by Well
normalize_dataframe Normalize
normalizingagents Normalizing Agents
normfluodat Cleans and normalizes DAT files obtained from experiments using the FLUOstar Omega microplate reader (from BMG LABTECH).
normfluodatfull Cleans and normalizes DAT files obtained from experiments using the FLUOstar Omega microplate reader (from BMG LABTECH).
normfluodatlite Cleans and normalizes DAT files obtained from experiments using the FLUOstar Omega microplate reader (from BMG LABTECH).
normfluodbf Cleans and Normalizes DBF files obtained from experiments using the FLUOstar Omega microplate reader (from BMG LABTECH).
normfluodbfplots Plot Plate - Favorite is Fluostar style
normfluordat Cleans and normalizes DAT files obtained from experiments using the FLUOstar Omega microplate reader (from BMG LABTECH).
normfluordbf Cleans and Normalizes DBF files obtained from experiments using the FLUOstar Omega microplate reader (from BMG LABTECH).
norm_tidy_dbf Cleans and Normalizes DBF files obtained from experiments using the FLUOstar Omega microplate reader (from BMG LABTECH).
norm_z Normalizing Agents
norm_z_df Normalizing Agents

-- O --

open_testfile Test Boilerplate

-- P --

parenttype Parent Type
parent_plate_type Parent Type
parent_plate_type.1536well_plate_t1 Parent Type
parent_plate_type.1536well_plate_t2 Parent Type
parent_plate_type.384well_plate Parent Type
parent_plate_type.96well_plate Parent Type
parent_plate_type.default Parent Type
parent_plate_type.normfluodbf_plate Parent Type
plate Plate
platedata Plate Data
platemeta Plate Meta
platename Plate Name
plate_data Plate Data
plate_data_summary Plate Data Summary
plate_meta Plate Meta
plate_meta.1536well_plate_t1 Plate Meta
plate_meta.1536well_plate_t2 Plate Meta
plate_meta.384well_plate Plate Meta
plate_meta.96well_plate Plate Meta
plate_meta.default Plate Meta
plate_types Plate Types Tibble
plate_types_tbl Plate Types Tibble
plate_types_vector Plate Types Tibble
plot.1536well_plate_t1 Plot Plate - Favorite is Fluostar style
plot.1536well_plate_t2 Plot Plate - Favorite is Fluostar style
plot.384well_plate Plot Plate - Favorite is Fluostar style
plot.96well_plate Plot Plate - Favorite is Fluostar style
print.1536well_plate_t1 Print
print.1536well_plate_t2 Print
print.384well_plate Print
print.96well_plate Print
printer Print

-- Q --

quiet Quiet

-- R --

removeoutliers Outliers
remove_leading_zero Format Well Names
remove_outliers Outliers
remove_outliers.1536well_plate_t1 Outliers
remove_outliers.1536well_plate_t2 Outliers
remove_outliers.384well_plate Outliers
remove_outliers.96well_plate Outliers
remove_outliers.default Outliers
replace_word_in_file Replace Word
resample_dat A function to create an attribute or column for each sample loaded into the microplate wells.
resample_dat_alt A function to create an attribute or column for each sample loaded into the microplate wells.
resample_dat_scale A function to create an attribute or column for each sample loaded into the microplate wells.
resample_dat_scale_alt A function to create an attribute or column for each sample loaded into the microplate wells.
resample_dat_scale_alt_bfv A function to create an attribute or column for each sample loaded into the microplate wells.
resample_dat_scale_alt_bf_na A function to create an attribute or column for each sample loaded into the microplate wells.
resample_dat_scale_alt_na A function to create an attribute or column for each sample loaded into the microplate wells.
resample_dat_scale_naretainer A function to create an attribute or column for each sample loaded into the microplate wells.
resample_dat_scale_optimus A function to create an attribute or column for each sample loaded into the microplate wells.
resample_dat_scale_optimus_backend A function to create an attribute or column for each sample loaded into the microplate wells.
resample_dat_scale_optimus_na A function to create an attribute or column for each sample loaded into the microplate wells.
resample_dat_vect A function to create an attribute or column for each sample loaded into the microplate wells.
resample_vect_scale A function to create an attribute or column for each sample loaded into the microplate wells.
reset_plate Plate
roundfluor Normalizing Agents
run_steps Steps Pipeline

-- S --

sampledata Get Development Data
sample_data_dir Get Development Data
sample_data_file Get Development Data
saveloadutils Save and Load Plate
save_plate Save and Load Plate
save_rds_plate Save and Load Plate
setsteps Set Plate Steps
setup_plate Plate
set_assiette_type Set The Plate Types
set_default_params Define Plate Parameters
set_default_status Define Plate Status
set_default_steps Define Plate Steps
set_plate_type Set The Child Plate Type
set_plate_version Plate Version
status Status
status<- Status
step Steps Utils
steps Set Plate Steps
steps<- Set Plate Steps
stepspipeline Steps Pipeline
stepsutils Steps Utils
steps_complete Steps Utils
step_begin Steps Utils
step_end Steps Utils
step_name Steps Utils

-- T --

test_boilerplate Test Boilerplate
type Plate Type

-- U --

update_status_list Define Plate Status
update_steps_list Define Plate Steps
uploadplatedata Upload Plate Data
upload_data Upload Plate Data
upload_data.1536well_plate_t1 Upload Plate Data
upload_data.1536well_plate_t2 Upload Plate Data
upload_data.384well_plate Upload Plate Data
upload_data.96well_plate Upload Plate Data
upload_data.default Upload Plate Data
use_initialized_plate Plate
use_setup_plate Plate

-- V --

var_str Save and Load Plate

-- X --

xycoordinates Plot Coordinates
x_var_one Plot Coordinates
x_var_one<- Plot Coordinates
x_var_one_label Plot Coordinates
x_var_one_label<- Plot Coordinates
x_var_two Plot Coordinates
x_var_two<- Plot Coordinates
x_var_two_label Plot Coordinates
x_var_two_label<- Plot Coordinates

-- Y --

y_var Plot Coordinates
y_var<- Plot Coordinates

-- misc --

%there% The %there% operator
.next_step Steps Pipeline
.step_name Steps Utils