Package: PKbioanalysis 0.5.0

Omar Elashkar

PKbioanalysis: Pharmacokinetic Bioanalysis Experiments Design and Exploration

Automate pharmacokinetic/pharmacodynamic bioanalytical procedures based on best practices and regulatory recommendations. The package impose regulatory constrains and sanity checking for common bioanalytical procedures. Additionally, 'PKbioanalysis' provides a relational infrastructure for plate management and injection sequence.

Authors:Omar Elashkar [aut, cre]

PKbioanalysis_0.5.0.tar.gz
PKbioanalysis_0.5.0.tar.gz(r-4.7-any)PKbioanalysis_0.5.0.tar.gz(r-4.6-any)
PKbioanalysis_0.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
PKbioanalysis/json (API)
NEWS

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

Bug tracker:https://github.com/omarashkar/pkbioanalysis/issues

Pkgdown/docs site:https://omarashkar.github.io

On CRAN:

Conda:

2.18 score 2 scripts 215 downloads 56 exports 145 dependencies

Last updated from:c61ca4f2b4. Checks:2 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64NOTE325
source / vignettesOK276
linux-release-x86_64NOTE345
wasm-releaseOK175

Exports:add_blankadd_cs_curveadd_DBadd_DQCadd_QCadd_samplesadd_samples_dbadd_suitabilityarea_report.PeakResbuild_injec_seqcalc_var_summarychrom_appcombine_injec_listscombine_platescreate_new_studycvdownload_sample_listestim_dil_limitestim_lloqexport_integrationexport_pk_profilesexport_runfill_schemefilter_chromfit_varformated_printgenerate_96get_compound_IDget_sample_IDget_sample_nameshas_default_boundsinstall_py_depintegrateis_integratedis_smoothedmake_calibration_studymake_metabolic_studynca_tableplate_metadataplate_treeplot_chromplot_peak_areas.PeakResplot_RT.PeakResplot_var_patternprecision_per_vialprefilter_precision_dataquant_appread_chromread_experiment_resultsregister_platereverse_predictrun_summarysmooth_chromstudy_appupdate_RTwrite_injec_seq

Dependencies:askpassassertthatbackportsbase64encbigDbitbit64bitopsbsiconsbslibcachemcheckmateclicliprcommonmarkcorocpp11crayoncrosstalkcurldata.tabledata.treeDBIDiagrammeRdigestdplyrDTduckdbellmerevaluatefarverfastmapfontawesomefontBitstreamVerafontLiberationfontquiverforcatsfsgdtoolsgenericsggforceggiraphggplot2gluegtgtablegtoolsherehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2igraphisobandjanitorjquerylibjsonlitejuicyjuiceknitrlabelinglaterlatticelazyevallearnrlifecyclelitedownlubridatemagrittrmarkdownMASSMatrixmemoisemimenlmenloptropensslotelpillarpkgconfigplotlypngpolyclippracmaprettyunitsprogresspromisespurrrR6RaMSrappdirsRColorBrewerRcppRcppEigenRcppTOMLreactablereactRreadrrenvreticulaterhandsontablerlangrmarkdownrprojrootrstudioapiRTMBS7sassscalesshinyshinyalertshinychatshinyjsshinyWidgetssnakecasesortablesourcetoolsstringistringrsyssystemfontstibbletidyrtidyselecttimechangetinytexTMBtweenrtzdbunitsutf8uuidV8vctrsviridisLitevisNetworkvroomwithrwritexlxfunxml2xtableyaml

Readme and manuals

Help Manual

Help pageTopics
Subsetting method for MultiPlate[[,MultiPlate-method
Add blank to the plate Can be either double blank (DB), CS0IS+ or CS+IS0add_blank
Add calibration curve to the plateadd_cs_curve
Add double blank (DB) to a plateadd_DB
Add dilution quality control (DQC) to the plateadd_DQC
Add quality control samples to the plateadd_QC
Add samples to plate with pharmacokinetic attributesadd_samples
Add samples from the sample log to the plateadd_samples_db
Add samples from the sample log to the plate with multiplicationadd_samples_db2
Add suitability sample to the plateadd_suitability
gt table of areasarea_report.PeakRes
Calculate Summary Statistics for Each Concentration Level For Either Concentration, Area, or Area Ratiocalc_var_summary
Check Matching of Compound and Transitions in chrom_res and method databasecheck_chrom_cmpds
chrom_appschrom_app
Create Sample List with rigorous designcombine_injec_lists
Combine plates in MultiPlate objectcombine_plates
Configure suitability runsconfig_suitability
Create a new study in the databasecreate_new_study
Calculate Coefficient of variationcv
Download sample list from database to local spreadsheet with vendor specific formatdownload_sample_list
Estimate Dilution Limit Based on Additive and Proportional Errors and LLOQestim_dil_limit
Estimate LLOQ From Existing Additive and Proportional errorsestim_lloq
Export Expected RTexport_integration
Export PK profiles for a given compound in a specified format Currently supports "nonmem" format. The exported file will include a CSV with the PK data and an Excel file with the codebook.export_pk_profiles
Export runexport_run
Extract Peak Boundariesextract_peak_bounds
Filling orientation of the platefill_scheme
title Filter Chromatogram Peaksfilter_chrom
Estimate Additive and proportional errors from calibration datafit_var
Format and print the results of fit_varformated_print
Generate 96 well plategenerate_96
Find Compound ID from compound Nameget_compound_ID
Find Sample ID from sample Nameget_sample_ID
Find sample names for all samplesget_sample_names
check if default expected RT is set for a compoundhas_default_bounds
Install Python dependencies for PKbioanalysisinstall_py_dep
integrate Peak with trapzoid method given start and endintegrate
Check if peak was integrated for a specific compoundis_integrated is_integrated,ChromRes-method is_integrated,ChromResBase-method
Return an indicator if the chromatogram is smoothedis_smoothed
Length method for MultiPlatelength,MultiPlate-method
Create a calibration study with calibration standards and QCsmake_calibration_study
Create a metabolic study layoutmake_metabolic_study
Calculate Cmax, Tmax and AUC for each subject given a compound's PK profilesnca_table
Merge PK profiles into QuantRes objectpkmerge
Set plate descriptionplate_metadata
Plot the design of the plateplate_tree
Plot Chromatogram per Sample for Selected transitionsplot_chrom
Plot peak areasplot_peak_areas.PeakRes
Plotting RT intervals of chromatogramplot_RT.ChromRes
Plot RTplot_RT.PeakRes
Plot Relationship Between Concentration and CV/SDplot_var_pattern
Plotting 96 well plateplot.PlateObj
Precision per vialprecision_per_vial
Filter dataprefilter_precision_data prefilter_precision_data,data.frame-method prefilter_precision_data,QuantRes-method
Quantification Appquant_app
Read Chromatogram Filesread_chrom
Read experiment resultsread_experiment_results
This will save the plate to the databaseregister_plate
Convert response to concentrationresponse_to_conc
Reverse predict concentration from responsereverse_predict
Get Summary of an objectrun_summary run_summary.PeakRes
Smooth Chromatogram Peakssmooth_chrom
bioanalytic_appstudy_app
Manually Update Observed RT for either all compounds, all next samples, or single compound and sampleupdate_RT
Write injection sequence to databasewrite_injec_seq