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

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

## Documentation for package ‘normfluodbf’ version 2.0.3

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A C D E F G H I L M N O P Q R S T U V W 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
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
find_random_port | Random Port Normfluodbf Style
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_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.
run_demo_bg | Run Demo Background
run_demo_in_background | Run Demo in Background
run_demo_script | Run Demo Script
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
shiny_random_port | Random Port gptstudio style
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
viewerpane_background_normfluodbf | View App in Viewer Pane

## -- W --

wait_for_bg_shinyapp | Validate URL

## -- 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