Package: tcpl 3.3.0.9000

Introduction | Suggested packages for use with this vignette | Overview | ToxCast Publications | Connection Configuration | Database Structure | Level 0 | SC Data-containing Tables | - Level 1 (sc1) | - Level 2 (sc1) | - Aggregated IDs (sc2_agg) | - Representative Samples (sc2_chid) | MC Data-containing Tables | - Level 1 (mc1) | - Level 2 (mc2) | - Level 3 (mc3) | - Aggregated IDs (mc4_agg) | - Level 4 (mc4) | - Level 4 Parameters (mc4_param) | - Level 5 (mc5) | - Level 5 Parameters (mc5_param) | - Representative Samples (mc5_chid) | - Level 6 (mc6) | - Level 7 (mc7) | Assay and Auxiliary Annotation Tables | - Assay_Source | - Assay | - Assay_Component | - Assay_Component_Endpoint | - Assay_Component_Map | - Assay_Descriptions | - Chemical | - Chemical_Lists | - Sample | Assay Registration | Assay Nomenclature | Minimum Required Fields | Assay Source | Assay | Assay Component | Assay Component Endpoint | Naming Revision | Chemical Registration | Chemicals | Samples | Chemical Lists | Level 0 Pre-Processing | Required Fields | Well Types | Writing New Data | Data Processing | Level IDs | Methods | Data Normalization | SC Data Processing | > Level 1 | - Methods Assignment | > Level 2 | - Overwrite Bidirectionality | MC Data Processing | > Level 3 | > Level 4 | - Pre-Modeling Processes | - Concentration-Response Modeling Details | - Curve Fitting | > Level 5 | -- Overwrite Bidirectionality Methods | -- LOEC Methods | - Winning Model Selection | - Level 6 | - Level 7 | Compiled Processing Examples | - SC Data | - MC Data | Data Interpretation | Hit Calls | Cutoff | Potency Estimates | Activity Concentrations at Specified Response | Benchmark Dose | LOEC | Fit Categories | Flags (Level 6) | Example of Flags | Representative Samples | MC Representative Samples | SC Representative Samples | Variable Matrices | Cytotoxicity Burst Distribution | Burst Endpoints | Implementation | Assay Description Documents | Administered Equivalent Doses | Options Applied | Analytical QC and Applicability Domain | Descriptions of Fields and Possible Options | Data Retrieval in invitrodb | Retrieving Assay Element IDs | Retrieving Assay Annotations | Retrieving Chemical Information | Retrieving Methods | Retrieving Data | Retrieving Level 0 Data | - Load SC0 Data | - Load MC0 Data | - Review MC assay quality | Retrieving SC Data and Methods | - Load SC2 Data | - Load SC Methods | Retrieving MC Data and Methods | - Load MC5 Data | - Load MC Methods | Data Retrieval via API | Assay Elements | Data | Assay Annotations | Retrieving Processed MC Data and Annotations | - By ID | - By level | Load aeid | Load acid | Load aid | Load asid | Load unit | Sample and Chemical information | Load concentration unit | Load chemical info | Plotting | Individual Plotting | - Output PDF of Verbose, Multiple Plots per Page, by aeid and/or spid | - Output Image File (JPG) of Single Verbose Plot, by aeid and spid | - Output to Console, by m4id or by aeid and spid | - Output PDF of Single Concentration Plots, Multiple Plots per Page, by aeid | Comparison Plotting | - Output PDF of Multiple Comparison Plots per Page, by aeid and Compared by spid | - Output PDF of Multiple Single Concentration Comparison Plots per Page, by aeid and Compared by spid | - Output PDF of Multiple Comparison Plots per Page, By aeid and Compared by Chemical | - Output Image File (JPG) of Single Expanded Comparison Plot by aeid | Advanced Comparison Plotting | API Configuration | - Output Image File (JPG) of Single Verbose Plot, by M4ID | - Output PDF of Multiple Comparison Plots per Page, By AEID and Compared by Chemical | Additional Examples | - Load Data for a Specific Chemical | - Plot Sample Subset | - Plot LOEC (Lowest Observed Effective Concentration) | Example Integrations with Other Computational Toxicology Tools | Evaluate ToxCast AEDs for a single chemical and target | Consider ToxRefDB in vivo toxicity benchmarks as POD-Traditional | Consider ToxCast in vitro bioactivity data as POD-NAM | Compare POD-Traditional with POD-NAM | Apply ToxCast to examine EcoTox hazard for a single chemical | Consider POD-NAM and POD-Traditional | Consider SeqAPASS | Consider EcoTox | Compare