1 - 9 of 9 results

TCPl / ToxCast Data Analysis Pipeline

A generalized platform for storing, normalizing, and dose-response modeling of large high-throughput and high-content chemical screening data. The tcpl package provides functionality for two screening paradigms: (i) single-concentration screening, intended to only identify potentially active compounds, and (ii) multiple-concentration screening intended to identify potentially active compounds and estimate the efficacy and potency through dose-response modeling. It also provides a categorization algorithm that segregates results into categories for rapid identification of potential false-positive and false-negative results.

QDREC / Quantal Dose Response Calculator

A web server for automatically determining quantal dose-response characteristics of macroparasites in phenotypic drug screening. Such parasites include the etiological agents of tropical diseases such as schistosomiasis, lymphatic filariasis, and onchocerciasis, which together afflict over 500 million people worldwide. Using a combination of biological imaging and supervised machine learning, QDREC automatically determines the number of parasites which differ significantly from controls at specific experimental conditions (e.g. compound and concentration). This statistic is then utilized to determine the corresponding quantitative dose-response characteristics of the parasite population.


Nonlinear dose-response models are primary tools for estimating the potency (e.g., half-maximum inhibitory concentration known as IC50) of anticancer drugs. drexplorer enables biologists to evaluate replicate reproducibility, detect outlier data points, fit different models, select the best model, estimate IC (inhibitory concentration) values at different percentiles, and assess drug-drug interactions. drexplorer serves as a computation engine within the R environment and a graphical interface for users who do not have programming backgrounds.

Dr Fit / Dose-Response FITting

Enables fitting dose-response curves with complex multiphasic features. Dr Fit is a software that reads the dose-response data and builds the model. The algorithm implemented in Dr-Fit first attempts to fit the data to a one process model. This is followed by an attempt to fit the data to a two inhibitory processes model. Then Dr-fit attempts to fit the data to a two processes model which includes a stimulatory process. Finally, the software attempts to fit the data to a three processes model, two of them being inhibitory (antagonist) and one stimulatory (agonist). Dr-Fit could be a useful tool for many experimentalists and analysts interested in the study of agent effects on biological systems.

BMDExpress Data Viewer

A web-based application for visualizing and graphing BMDExpress output files. BMDExpress applies BMD modeling to transcriptomic datasets to identify transcriptional BMDs. Through our case studies, we demonstrate that BMDExpress Data Viewer is a useful tool to visualize, explore and analyze BMDExpress output files. Visualizing the data in this manner enables rapid assessment of data quality, model fit, doses of peak activity, most sensitive pathway perturbations and other metrics that will be useful in applying toxicogenomics in risk assessment.