Analysis of Broth Microdilution Assays

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Documentation for package ‘microdiluteR’ version 1.0.1

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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.