Learn R Programming

toxplot (version 0.1.1)

Batch Processing, Modeling and Visualizing the Dose-Response of High-Throughput Screening Bioassay

Description

A convenient interface to batch process high-throughput toxicology bioassay screening data. It's designed specifically for screening experiment that features a primary inhibition-type assay and a companion cytotoxicity assay. This package provides functions for data normalization, quality-control analysis, dose-response curve fitting (using the Hill model provided in the 'tcpl' package), visualization, and a unique toxicity-adjusted potency ranking system.

Copy Link

Version

Install

install.packages('toxplot')

Monthly Downloads

1

Version

0.1.1

License

GPL (>= 2)

Issues

Pull Requests

Stars

Forks

Maintainer

Jun Wang

Last Published

April 3rd, 2018

Functions in toxplot (0.1.1)

hill_model

hill mode in ToxCast tcpl package
demo_mc_norm

Normalized example multi-concentration screening data
log_abs_ec

calculate absolute EC_anything based on tcpl hill model
normalize_per_plate

normalize per plate
normalize_single_assay

normalize per plate (from single assay data)
plot_tcpl

Plot dose-resonse curves based on the tcpl hill model
plot_tcpl_minimal

Plot dose-resonse curves with minimal text annotation This funciton plots dose-response curve with minimal text annotation, no x and y axis label, 0 borders. Useful when need to present several plots together.
summary_tcpl

function to summarize curve fitting results
auc_hill_tcpl

function to calculate Area Under the Curve (AUC) of the hill model
fit_curve_tcpl

fit dose-resopnse curve using tcpl hill model
qc_per_plate

Quality-control metrics calculation
demo_mc

Example multi-concentration screening data
rank_tcpl

function to calculate ranking score, TAA, med_diff, EC values based on tcpl hill model
round_df

round digits of numbers
save_plot_pdf

save plots in pdf