Package: ccdR 1.1.0

Paul Kruse

ccdR: Utilities for Interacting with the 'CTX' APIs

Access chemical, hazard, bioactivity, and exposure data from the Computational Toxicology and Exposure ('CTX') APIs <https://api-ccte.epa.gov/docs/>. 'ccdR' was developed to streamline the process of accessing the information available through the 'CTX' APIs without requiring prior knowledge of how to use APIs. Most data is also available on the CompTox Chemical Dashboard ('CCD') <https://comptox.epa.gov/dashboard/> and other resources found at the EPA Computational Toxicology and Exposure Online Resources <https://www.epa.gov/comptox-tools>.

Authors:Paul Kruse [aut, cre], Caroline Ring [aut], Madison Feshuk [ctb], Carter Thunes [ctb], Jason Brown [ctb]

ccdR_1.1.0.tar.gz
ccdR_1.1.0.zip(r-4.5)ccdR_1.1.0.zip(r-4.4)ccdR_1.1.0.zip(r-4.3)
ccdR_1.1.0.tgz(r-4.4-any)ccdR_1.1.0.tgz(r-4.3-any)
ccdR_1.1.0.tar.gz(r-4.5-noble)ccdR_1.1.0.tar.gz(r-4.4-noble)
ccdR_1.1.0.tgz(r-4.4-emscripten)ccdR_1.1.0.tgz(r-4.3-emscripten)
ccdR.pdf |ccdR.html
ccdR/json (API)
NEWS

# Install 'ccdR' in R:
install.packages('ccdR', repos = c('https://usepa.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/usepa/ccdr/issues

Datasets:

On CRAN:

6.68 score 2 stars 7 scripts 579 downloads 86 exports 32 dependencies

Last updated 4 months agofrom:9efb857b39. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 06 2024
R-4.5-winOKNov 06 2024
R-4.5-linuxOKNov 06 2024
R-4.4-winOKNov 06 2024
R-4.4-macOKNov 06 2024
R-4.3-winOKNov 06 2024
R-4.3-macOKNov 06 2024

Exports:ccdr_hide_api_keyccdr_show_api_keychemical_containschemical_contains_batchchemical_equalchemical_equal_batchchemical_starts_withchemical_starts_with_batchctx_keyget_all_assaysget_all_public_chemical_listsget_annotation_by_aeidget_annotation_by_aeid_batchget_bioactivity_detailsget_bioactivity_details_batchget_bioactivity_endpoint_statusget_bioactivity_summaryget_bioactivity_summary_batchget_cancer_hazardget_cancer_hazard_batchget_chem_infoget_chem_info_batchget_chemical_by_property_rangeget_chemical_by_property_range_batchget_chemical_detailsget_chemical_details_batchget_chemical_endpoint_statusget_chemical_imageget_chemical_image_batchget_chemical_lists_by_typeget_chemical_lists_by_type_batchget_chemical_molget_chemical_mol_batchget_chemical_mrvget_chemical_mrv_batchget_chemical_synonymget_chemical_synonym_batchget_chemicals_in_listget_chemicals_in_list_batchget_ecotox_hazard_by_dtxsidget_ecotox_hazard_by_dtxsid_batchget_exposure_endpoint_statusget_exposure_functional_useget_exposure_functional_use_batchget_exposure_functional_use_categoryget_exposure_functional_use_probabilityget_exposure_functional_use_probability_batchget_exposure_list_presence_tagsget_exposure_list_presence_tags_by_dtxsidget_exposure_list_presence_tags_by_dtxsid_batchget_exposure_product_dataget_exposure_product_data_batchget_exposure_product_data_pucget_fate_by_dtxsidget_fate_by_dtxsid_batchget_genetox_detailsget_genetox_details_batchget_genetox_summaryget_genetox_summary_batchget_hazard_by_dtxsidget_hazard_by_dtxsid_batchget_hazard_endpoint_statusget_human_hazard_by_dtxsidget_human_hazard_by_dtxsid_batchget_inchiget_inchikeyget_lists_containing_chemicalget_lists_containing_chemical_batchget_msready_by_dtxcidget_msready_by_dtxcid_batchget_msready_by_formulaget_msready_by_formula_batchget_msready_by_massget_msready_by_mass_batchget_msready_by_mass_with_error_batchget_public_chemical_list_by_nameget_public_chemical_list_by_name_batchget_skin_eye_hazardget_skin_eye_hazard_batchget_smileshas_ccdr_optionhas_ccdr_optionshas_ctx_keyregister_ccdrset_ccdr_optionshowing_key

Dependencies:askpassclicpp11curldata.tabledplyrfansigenericsgluehttrjsonlitelifecyclemagrittrmimeopensslpillarpkgconfigpurrrR6Rcpprlangstringistringrsystibbletidyrtidyselecttriebeardurltoolsutf8vctrswithr

Getting started with ccdR: Introduction Vignette

Rendered fromIntroduction.Rmdusingknitr::rmarkdownon Nov 06 2024.

Last update: 2024-06-27
Started: 2024-03-07

Bioactivity API

Rendered fromBioactivity.Rmdusingknitr::rmarkdownon Nov 06 2024.

Last update: 2024-06-27
Started: 2024-03-01

Chemical API

Rendered fromChemical.Rmdusingknitr::rmarkdownon Nov 06 2024.

Last update: 2024-07-09
Started: 2024-03-01

Exposure API

Rendered fromExposure.Rmdusingknitr::rmarkdownon Nov 06 2024.

Last update: 2024-06-27
Started: 2024-06-05

Hazard API

Rendered fromHazard.Rmdusingknitr::rmarkdownon Nov 06 2024.

Last update: 2024-06-27
Started: 2024-03-01

Readme and manuals

Help Manual

Help pageTopics
Bioactivity API Server urlbioactivity_api_server
ccdr Optionsccdr_options has_ccdr_option has_ccdr_options set_ccdr_option
Chemical API Server urlchemical_api_server
Chemical containschemical_contains
Chemical contains batch searchchemical_contains_batch
Chemical equalchemical_equal
Chemical equal batch searchchemical_equal_batch
Chemical starts withchemical_starts_with
Chemical starts with batch searchchemical_starts_with_batch
Create chemical details data.table helper functioncreate_data.table_chemical_details
Exposure API Server urlexposure_api_server
Retrieve all assaysget_all_assays
Get all public chemical listsget_all_public_chemical_lists
Retrieve annotations for AEIDget_annotation_by_aeid
Retrieve annotations for AEID batchget_annotation_by_aeid_batch
Retrieve bioactivity data from DTXSID, AEID, SPID, or m4idget_bioactivity_details
Retrieve bioactivity data from DTXSID or AEID batchget_bioactivity_details_batch
Bioactivity API Endpoint statusget_bioactivity_endpoint_status
Retrieve bioactivity summary for AEIDget_bioactivity_summary
Retrieve bioactivity summary data from AEID batchget_bioactivity_summary_batch
Get cancer hazardget_cancer_hazard
Get cancer hazard batchget_cancer_hazard_batch
Get cancer hazard batchget_cancer_hazard_batch_old
Retrieve chemical informationget_chem_info
Retrieve chemical information in batch searchget_chem_info_batch
Retrieve chemical information in batch searchget_chem_info_batch_old
Get chemicals by property and its value rangeget_chemical_by_property_range
Retrieve chemicals by property and value range in batch searchget_chemical_by_property_range_batch
Retrieve chemical details from DTXSID of DTXCIDget_chemical_details
Retrieve chemical details from DTXSID of DTXCID in batch searchget_chemical_details_batch
Chemical API Endpoint statusget_chemical_endpoint_status
Get image file by DTXSID or DTXCIDget_chemical_image
Get image file by DTXSID or DTXCID batchget_chemical_image_batch
Get chemical lists by typeget_chemical_lists_by_type
Get chemical lists by type batch searchget_chemical_lists_by_type_batch
Get mol file by DTXSID or DTXCIDget_chemical_mol
Get mol file by DTXSID or DTXCID batchget_chemical_mol_batch
Get mrv file by DTXSID or DTXCIDget_chemical_mrv
Ger mrv file by DTXSID or DTXCID batchget_chemical_mrv_batch
Get chemical synonymget_chemical_synonym
Get chemical synonym batchget_chemical_synonym_batch
Get chemicals in a given chemical listget_chemicals_in_list
Get chemicals in a given chemical list batchget_chemicals_in_list_batch
Get ecotox hazard data by DTXSIDget_ecotox_hazard_by_dtxsid
Get ecotox hazard data by DTXSID batchget_ecotox_hazard_by_dtxsid_batch
Get ecotox hazard data by DTXSID batchget_ecotox_hazard_by_dtxsid_batch_old
Exposure API Endpoint statusget_exposure_endpoint_status
Retrieve exposure related functional use dataget_exposure_functional_use
Retrieve exposure related functional use data batchget_exposure_functional_use_batch
Retrieve functional use categoriesget_exposure_functional_use_category
Retrieve probability of exposure for functional use categoryget_exposure_functional_use_probability
Retrieve exposure functional use probability data batchget_exposure_functional_use_probability_batch
Retrieve list presence tagsget_exposure_list_presence_tags
Retrieve document data and list presence tags for a chemicalget_exposure_list_presence_tags_by_dtxsid
Retrieve document data and list presence tags for chemicals batchget_exposure_list_presence_tags_by_dtxsid_batch
Retrieve product data for exposure purposesget_exposure_product_data
Retrieve product data for exposure purposes batchget_exposure_product_data_batch
Retrieve product use categories related to exposureget_exposure_product_data_puc
Get fate by DTXSIDget_fate_by_dtxsid
Retrieve chemical fate data in batch searchget_fate_by_dtxsid_batch
Retrieve chemical fate data in batch searchget_fate_by_dtxsid_batch_old
Get genetox detailsget_genetox_details
Get genetox details batchget_genetox_details_batch
Get genetox details batchget_genetox_details_batch_old
Get genetox summaryget_genetox_summary
Get genetox summary batchget_genetox_summary_batch
Get genetox summary batchget_genetox_summary_batch_old
Get hazard data by DTXSIDget_hazard_by_dtxsid
Get hazard data by DTXSID batchget_hazard_by_dtxsid_batch
Get hazard data by DTXSID batchget_hazard_by_dtxsid_batch_old
Hazard API Endpoint statusget_hazard_endpoint_status
Get human hazard data by DTXSIDget_human_hazard_by_dtxsid
Get human hazard data by DTXSID batchget_human_hazard_by_dtxsid_batch
Get human hazard data by DTXSID batchget_human_hazard_by_dtxsid_batch_old
Get InChIget_inchi
Get InChIKeyget_inchikey
Get chemical lists containing given chemicalget_lists_containing_chemical
Get chemical lists containing given chemical batchget_lists_containing_chemical_batch
Get msready by DTXCIDget_msready_by_dtxcid
Get msready by DTXCID batch searchget_msready_by_dtxcid_batch
Get msready by formulaget_msready_by_formula
Get msready by formula batch searchget_msready_by_formula_batch
Get msready by massget_msready_by_mass
Get ms ready by mass batch searchget_msready_by_mass_batch
Get msready by mass and error offsetget_msready_by_mass_with_error_batch
Get chemical list by nameget_public_chemical_list_by_name
Get chemical list by name batchget_public_chemical_list_by_name_batch
Get skin and eye hazardget_skin_eye_hazard
Get skin and eye hazard batchget_skin_eye_hazard_batch
Get skin and eye hazard batchget_skin_eye_hazard_batch_old
Get Smilesget_smiles
Hazard API Server urlhazard_api_server
Prepare url helper functionprepare_word
Register a CTX APIccdr_hide_api_key ccdr_show_api_key ctx_key has_ctx_key print.ctx_credentials register_ccdr showing_key