R: Analysis of Broth Microdilution Assays

# Analysis of Broth Microdilution Assays

## Documentation for package ‘microdiluteR’ version 1.0.1

- DESCRIPTION file
- Package README

## Help Pages

add_concentration | Add concentration metadata
add_treatment | Add treatment metadata
apply_sign_test | Apply sign test
apply_validation_method | Check validity of each cell in data frame.
ask_concentration_list | Add concentration metadata
ask_experiment_list | Generate list of experiment names from user parameters
ask_group_list | Generate list of group IDs from user parameters
ask_invalid_samples | Check validity of each cell in data frame.
ask_threshold | Check validity of each cell in data frame.
ask_treatment_list | Add treatment metadata
ask_validity_method | Check validity of each cell in data frame.
bma | Absorption values from six broth microdilution assays conducted on 96-well plates
calculate_growth_performance | Calculate and visualize growth performance
calculate_percentage_change | Calculate and visualize growth performance
check_monotonicity | Check monotonicity of well positions across groups
check_well_positions | Check monotonicity of well positions across groups
generate_concentration_list | Add concentration metadata
generate_experiment_list | Generate list of experiment names from user parameters
generate_group_list | Generate list of group IDs from user parameters
generate_treatment_list | Add treatment metadata
match_concentration | Add concentration metadata
match_treatment | Add treatment metadata
plot_growth_performance | Calculate and visualize growth performance
read_plate | Read multiple text files from photometer measurement
read_plates | Read multiple text files from photometer measurement
subtract_T0 | Subtract timepoint T0 and remove from data
summarise_growth_performance | Calculate and visualize growth performance
summarize_growth_performance | Calculate and visualize growth performance
tidy_plates | Add metadata to values from photometer measurements
tidy_plates_via_params | Tidy multiple 96-well plates via parameters
tidy_plates_via_prompts | Read raw photometry data and add meta data based on user input
tidy_single_plate | Tidy single 96-well plate via parameters
update_validity | Check validity of each cell in data frame.
validate_cells | Check validity of each cell in data frame.