Datasets

Test-post_file_tags

Assay Description Documents

This documentation for the ToxCast assay endpoints is in a format outlined by the OECD Guidance Document 211 (GD211) for describing non-guideline in vitro test methods and their interpretation. The intent of GD 211 is to harmonize non-guideline, in vitro method descriptions to allow assessment of the relevance of the test method for biological responses of interest and the quality of the data produced. This dataset contains reports for 809 assay endpoints accompanying the invitrodb v4.2 release (Sept 2024). Compiled report is available here: (INSERT LINK). These reports are a work in progress and will be iteratively updated as more information becomes available. Please cite as: "US EPA (2024). ToxCast Assay Description Documentation. EPA Publication Number 601B24001. https://doi.org/10.23645/epacomptox.6328037.v11"

MMDB v1.0 Scripts

Contains all scripts associated with the v1.0 release of MMDB. These were previously organized into the following datasets: MMDB Processing Scripts, Sample Queries (example queries for exploring the MMDB database), & MMDB Correction Scripts (a set of SQL commands to run to update the associated MMDB SQL dump version - these help fix minor curation issues identified after the dump file was created).

Release_Note

This .html output from Rmarkdown that describes the update of invitrodb between versions 4.1 and 4.2. Invitrodb v4.2 represents the second full release of the ToxCast database in a new schema designed to accommodate the R package dependency, tcplFit2, which is used in curve-fitting and hit-calling of multi-concentration response data. This invitrodb schema was beta-tested with our research release of invitrodb v4.0 that accompanied the publication "The ToxCast Pipeline: Updates to Curve-Fitting Approaches and Database Structure" (Feshuk et al., 2023 https://www.frontiersin.org/journals/toxicology/articles/10.3389/ftox.2023.1275980) and release of tcpl v3.0.1.

MySQL_Data

This includes a sql dump of invitrodb v4.2 with installation instructions available in README.

Summary_Files

This includes a zip file of summary files with descriptions available in README. Corrections: -Uploaded v4.2 tcplVarMat output (variable matrices of hitcalls, ACCs and AC50s)

Plots

This includes a zip file of plots by assay source. Note: X axis of "Concentration (.M)" should be "Concentration (μM)" on all plots.

Previous Data

Abstract Sifter Plus

Files and videos for Abstract Sifter Plus.

EDSP

Policy Use Documents - Dev New

Eco-HTTr data analysis pipeline

This dataset provides the code-base for RNAseq data pipelining and analysis as part of the U.S. EPA, Great Lakes Toxicology and Ecology Division's ecological high throughput transcriptomics research program. The scripts are designed for use in either the U.S. EPA High Performance Computing (HPC) system or in R/R-studio. The scripts cover the entire workflow, starting with raw FASTQ files, to data preprocessing and quality control to differential gene expression analysis, benchmark dose modeling, and functional enrichment analysis. The code is accompanied by a protocol designed to be accessible to researchers with no prior experience in coding or working within a Linux-based computing environment. It aims to provide detailed, step-by-step instructions that will enable users to navigate through the various stages of the analysis pipeline effectively.