Files in USEPA/CompTox-ToxCast-tcpl
ToxCast Data Analysis Pipeline
.Rbuildignore
.github/workflows/test-on-PR.yaml
.gitignore
CONTRIBUTING.md
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
NEWS
R/Models.R
R/assay_funcs.R
R/attachFormals.R
R/blineShift.R
R/buildAssayQ.R
R/chemQueries.R
R/clearSQLite.R
R/config_funcs.R
R/convertNames.R
R/data.R
R/drawCircles.R
R/flareFunc.R
R/getConfFile.R
R/hill_utils.R
R/interlaceFunc.R
R/is.odd.R
R/load6DR.R
R/lu.R
R/lw.R
R/mc1.R
R/mc2.R
R/mc2_mthds.R
R/mc3.R
R/mc3_mthds.R
R/mc4.R
R/mc4_mthds.R
R/mc5.R
R/mc5_mthds.R
R/mc6.R
R/mc6_mthds.R
R/mthd_funcs.R
R/multProc.R
R/multiplotFit.R
R/onAttach.R
R/onLoad.R
R/plateHeat.R
R/plotCompareFit.R
R/plotFit.R
R/prepField.R
R/query_funcs.R
R/registerMthd.R
R/rgstr_funcs.R
R/sc1.R
R/sc1_mthds.R
R/sc2.R
R/sc2_mthds.R
R/sink.reset.R
R/tcplAICProb.R
R/tcplAddModel.R
R/tcplAppend.R
R/tcplCascade.R
R/tcplCode2CASN.R
R/tcplConf.R
R/tcplConfDefault.R
R/tcplConfExample.R
R/tcplConfList.R
R/tcplConfLoad.R
R/tcplConfReset.R
R/tcplConfSave.R
R/tcplCytoPt.R
R/tcplDefine.R
R/tcplDelete.R
R/tcplFit.R
R/tcplFit2.R
R/tcplGetAeid.R
R/tcplHillACXX.R
R/tcplHillConc.R
R/tcplHillVal.R
R/tcplListFlds.R
R/tcplLiteInit.R
R/tcplLoadAcid.R
R/tcplLoadAeid.R
R/tcplLoadAid.R
R/tcplLoadAsid.R
R/tcplLoadChem.R
R/tcplLoadClib.R
R/tcplLoadConcUnit.R
R/tcplLoadData.R
R/tcplLoadUnit.R
R/tcplLvlCount.R
R/tcplMakeAeidMultiPlts.R
R/tcplMakeAeidPlts.R
R/tcplMakeChidMultiPlts.R
R/tcplMthdAssign.R
R/tcplMthdClear.R
R/tcplMthdList.R
R/tcplMthdLoad.R
R/tcplMultiplot.R
R/tcplObjCnst.R
R/tcplObjGnls.R
R/tcplObjHill.R
R/tcplPlot.R
R/tcplPlotFitc.R
R/tcplPlotFits.R
R/tcplPlotM4ID.R
R/tcplPlotPlate.R
R/tcplPrepOtpt.R
R/tcplQuery.R
R/tcplQueryAPI.R
R/tcplRegister.R
R/tcplRun.R
R/tcplSendQuery.R
R/tcplSubsetChid.R
R/tcplUpdate.R
R/tcplVarMat.R
R/tcplWriteData.R
R/tcplWriteLvl0.R
R/tcpldbStats.R
R/v3_schema_functions.R
README.md
cran-comments.md
data-raw/mc_vignette.R
data-raw/mc_vignette.Rout
data-raw/sample_data_dictionary.R
data-raw/sc_vignette.R
data-raw/sc_vignette.Rout
data-raw/tcplLoadData_columns.R
data/chdat.rda
data/invitrodb_dd.rda
data/load_data_columns.rda
data/mc_vignette.rda
data/mcdat.rda
data/sc_vignette.rda
data/scdat.rda
inst/TCPL.config
inst/csv/assay.csv
inst/csv/assay_component.csv
inst/csv/assay_component_endpoint.csv
inst/csv/assay_component_map.csv
inst/csv/assay_reagent.csv
inst/csv/assay_source.csv
inst/csv/chemical.csv
inst/csv/chemical_library.csv
inst/csv/mc0.csv
inst/csv/mc1.csv
inst/csv/mc2.csv
inst/csv/mc2_acid.csv
inst/csv/mc2_methods.csv
inst/csv/mc3.csv
inst/csv/mc3_aeid.csv
inst/csv/mc3_methods.csv
inst/csv/mc4.csv
inst/csv/mc4_aeid.csv
inst/csv/mc4_agg.csv
inst/csv/mc4_methods.csv
inst/csv/mc5.csv
inst/csv/mc5_aeid.csv
inst/csv/mc5_chid.csv
inst/csv/mc5_fit_categories.csv
inst/csv/mc5_methods.csv
inst/csv/mc6.csv
inst/csv/mc6_aeid.csv
inst/csv/mc6_methods.csv
inst/csv/sample.csv
inst/csv/sc0.csv
inst/csv/sc1.csv
inst/csv/sc1_aeid.csv
inst/csv/sc1_methods.csv
inst/csv/sc2.csv
inst/csv/sc2_aeid.csv
inst/csv/sc2_agg.csv
inst/csv/sc2_methods.csv
inst/example/assay.csv
inst/example/assay_component.csv
inst/example/assay_component_endpoint.csv
inst/example/assay_component_map.csv
inst/example/assay_source.csv
inst/example/chemical.csv
inst/example/chemical_library.csv
inst/example/mc0.csv
inst/example/mc1.csv
inst/example/mc2.csv
inst/example/mc2_acid.csv
inst/example/mc2_methods.csv
inst/example/mc3.csv
inst/example/mc3_aeid.csv
inst/example/mc3_methods.csv
inst/example/mc4.csv
inst/example/mc4_aeid.csv
inst/example/mc4_agg.csv
inst/example/mc4_methods.csv
inst/example/mc5.csv
inst/example/mc5_aeid.csv
inst/example/mc5_fit_categories.csv
inst/example/mc5_methods.csv
inst/example/mc6.csv
inst/example/mc6_aeid.csv
inst/example/mc6_methods.csv
inst/example/sample.csv
inst/example/sc0.csv
inst/example/sc1.csv
inst/example/sc1_aeid.csv
inst/example/sc1_methods.csv
inst/example/sc2.csv
inst/example/sc2_aeid.csv
inst/example/sc2_agg.csv
inst/example/sc2_methods.csv
man-roxygen/loadlvl.R
man-roxygen/proclvl.R
man/MC2_Methods.Rd
man/MC3_Methods.Rd
man/MC4_Methods.Rd
man/MC5_Methods.Rd
man/MC6_Methods.Rd
man/Models.Rd
man/SC1_Methods.Rd
man/SC2_Methods.Rd
man/assay_funcs.Rd
man/blineShift.Rd
man/chdat.Rd
man/check_tcpl_db_schema.Rd
man/config_funcs.Rd
man/dot-buildAssayQ.Rd
man/dot-convertNames.Rd
man/dot-load6DR.Rd
man/dot-plateHeat.Rd
man/dot-prepField.Rd
man/flareFunc.Rd
man/hill_utils.Rd
man/interlaceFunc.Rd
man/invitrodb_dd.Rd
man/is.odd.Rd
man/load_data_columns.Rd
man/lu.Rd
man/lw.Rd
man/mc1.Rd
man/mc2.Rd
man/mc3.Rd
man/mc4.Rd
man/mc5.Rd
man/mc6.Rd
man/mc_vignette.Rd
man/mcdat.Rd
man/mthd_funcs.Rd
man/query_funcs.Rd
man/registerMthd.Rd
man/rgstr_funcs.Rd
man/sc1.Rd
man/sc2.Rd
man/sc_vignette.Rd
man/scdat.Rd
man/sink.reset.Rd
man/tcplAICProb.Rd
man/tcplAddModel.Rd
man/tcplAppend.Rd
man/tcplCascade.Rd
man/tcplCode2CASN.Rd
man/tcplCytoPt.Rd
man/tcplDefine.Rd
man/tcplDelete.Rd
man/tcplFit.Rd
man/tcplFit2.Rd
man/tcplFit2_nest.Rd
man/tcplFit2_unnest.Rd
man/tcplGetAeid.Rd
man/tcplHit2.Rd
man/tcplListFlds.Rd
man/tcplLoadChem.Rd
man/tcplLoadClib.Rd
man/tcplLoadConcUnit.Rd
man/tcplLoadData.Rd
man/tcplLoadUnit.Rd
man/tcplLvlCount.Rd
man/tcplMakeAeidMultiPlts.Rd
man/tcplMakeAeidPlts.Rd
man/tcplMakeChidMultiPlts.Rd
man/tcplMultiplot.Rd
man/tcplPlot.Rd
man/tcplPlotFitc.Rd
man/tcplPlotFits.Rd
man/tcplPlotM4ID.Rd
man/tcplPlotPlate.Rd
man/tcplPlotlyPlot.Rd
man/tcplPrepOtpt.Rd
man/tcplRun.Rd
man/tcplSubsetChid.Rd
man/tcplVarMat.Rd
man/tcplWriteData.Rd
man/tcplWriteLvl0.Rd
man/tcpldbStats.Rd
man/tcplggplot.Rd
man/tcplggplotCompare.Rd
man/write_lvl_4.Rd
tests/testthat.R
tests/testthat/_snaps/tcplDefine.md
tests/testthat/_snaps/tcplPlot/negative-cutoff-bmr.svg
tests/testthat/_snaps/tcplPlot/test-output-482273.svg
tests/testthat/helper-functions.R
tests/testthat/test-plotting.R
tests/testthat/test-tcplConf.R
tests/testthat/test-tcplDefine.R
tests/testthat/test-tcplLoadData.R
tests/testthat/test-tcplPlot.R
vignettes/.gitignore
vignettes/Assay_Registration.Rmd
vignettes/Data_processing-Archive_tcpl_v2.Rmd
vignettes/Data_processing.Rmd
vignettes/Data_retrieval.Rmd
vignettes/Introduction_Appendices.Rmd
vignettes/img/Fig1_tcpl_overview.png
vignettes/img/Fig5_fitc_tree_10jul2023.png
vignettes/img/ccd_seqapass_filter.png
vignettes/img/output_console.png
vignettes/img/output_jpg.jpg
vignettes/img/output_pdf.png
