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PKbioanalysis

PKbioanalysis is a comprehensive R package designed to streamline pharmacokinetic (PK) and bioanalytical workflows from study design through data analysis and reporting. Built on regulatory best practices and FAIR principles, it provides an integrated solution for managing bioanalytical experiments with persistent data storage, interactive visualizations, and AI-assisted quality control.

✨ Key Features

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Install

install.packages('PKbioanalysis')

Monthly Downloads

575

Version

0.5.0

License

AGPL (>= 3)

Maintainer

Omar Elashkar

Last Published

February 17th, 2026

Functions in PKbioanalysis (0.5.0)

title Filter Chromatogram Peaks

Utility to extract named xml child to dataframe and rename

Filling orientation of the plate

extract_peak_bounds

Extract Peak Boundaries

Estimate Additive and proportional errors from calibration data

Return an indicator if the chromatogram is smoothed

Check if peak was integrated for a specific compound

.parse_tlynx_xml

Parse targetlynx

get_sample_names

Find sample names for all samples

plot_var_pattern

Plot Relationship Between Concentration and CV/SD

precision_per_vial

Precision per vial

has_default_bounds

check if default expected RT is set for a compound

Plot Chromatogram per Sample for Selected transitions

make_metabolic_study

Create a metabolic study layout

plot_peak_areas.PeakRes

Plot peak areas

Calculate Cmax, Tmax and AUC for each subject given a compound's PK profiles

integrate Peak with trapzoid method given start and end

Install Python dependencies for PKbioanalysis

Set plate description

Merge PK profiles into QuantRes object

Plotting 96 well plate

plot_RT.ChromRes

Plotting RT intervals of chromatogram

Read Chromatogram Files

Quantification App

export_pk_profiles

Export PK profiles for a given compound in a specified format Currently supports "nonmem" format. The exported file will include a CSV with the PK data and an Excel file with the codebook.

plot_RT.PeakRes

Plot the design of the plate

prefilter_precision_data

length,MultiPlate-method

Length method for MultiPlate

make_calibration_study

Create a calibration study with calibration standards and QCs

read_experiment_results

Read experiment results

register_plate,MultiPlate-method

Register a multiple plates at once

Smooth Chromatogram Peaks

bioanalytic_app

reverse_predict

Reverse predict concentration from response

register_plate,PlateObj-method

Register a plate This will save the plate to the database

This will save the plate to the database

write_injec_seq

Write injection sequence to database

Get Summary of an object

response_to_conc

Convert response to concentration

[[,MultiPlate-method

Subsetting method for MultiPlate

Manually Update Observed RT for either all compounds, all next samples, or single compound and sample

add_samples_db2

Add samples from the sample log to the plate with multiplication

Add samples to plate with pharmacokinetic attributes

Add samples from the sample log to the plate

Add double blank (DB) to a plate

Add blank to the plate Can be either double blank (DB), CS0IS+ or CS+IS0

Add calibration curve to the plate

add_suitability

Add suitability sample to the plate

Add dilution quality control (DQC) to the plate

Add quality control samples to the plate

combine_injec_lists

Create Sample List with rigorous design

config_suitability

Configure suitability runs

calc_var_summary

Calculate Summary Statistics for Each Concentration Level For Either Concentration, Area, or Area Ratio

check_chrom_cmpds

Check Matching of Compound and Transitions in chrom_res and method database

create_new_study

Create a new study in the database

get_compound_ID

Find Compound ID from compound Name

Find Sample ID from sample Name

area_report.PeakRes

gt table of areas

PKbioanalysis-package

PKbioanalysis: Pharmacokinetic Bioanalysis Experiments Design and Exploration

Combine plates in MultiPlate object

build_injec_seq

Create Injection Sequence

Calculate Coefficient of variation

.parse_tlynx_csv

Parse targetlynx CSV file

Create a new methods database from a YAML file

Filter peaks to specific RT range

Format and print the results of fit_var

estim_dil_limit

Estimate Dilution Limit Based on Additive and Proportional Errors and LLOQ

Generate 96 well plate

clear_python_deps

Clear Managed Python Environments

export_integration

Export Expected RT

Estimate LLOQ From Existing Additive and Proportional errors

download_sample_list

Download sample list from database to local spreadsheet with vendor specific format