Package: Rcurvep 1.3.1

Rcurvep: Concentration-Response Data Analysis using Curvep

An R interface for processing concentration-response datasets using Curvep, a response noise filtering algorithm. The algorithm was described in the publications (Sedykh A et al. (2011) <doi:10.1289/ehp.1002476> and Sedykh A (2016) <doi:10.1007/978-1-4939-6346-1_14>). Other parametric fitting approaches (e.g., Hill equation) are also adopted for ease of comparison. 3-parameter Hill equation from 'tcpl' package (Filer D et al., <doi:10.1093/bioinformatics/btw680>) and 4-parameter Hill equation from Curve Class2 approach (Wang Y et al., <doi:10.2174/1875397301004010057>) are available. Also, methods for calculating the confidence interval around the activity metrics are also provided. The methods are based on the bootstrap approach to simulate the datasets (Hsieh J-H et al. <doi:10.1093/toxsci/kfy258>). The simulated datasets can be used to derive the baseline noise threshold in an assay endpoint. This threshold is critical in the toxicological studies to derive the point-of-departure (POD).

Authors:Jui-Hua Hsieh [aut, cre], Alexander Sedykh [aut], Fred Parham [ctb], Yuhong Wang [ctb], Tongan Zhao [aut], Ruili Huang [ctb]

Rcurvep_1.3.1.tar.gz
Rcurvep_1.3.1.zip(r-4.5)Rcurvep_1.3.1.zip(r-4.4)Rcurvep_1.3.1.zip(r-4.3)
Rcurvep_1.3.1.tgz(r-4.4-any)Rcurvep_1.3.1.tgz(r-4.3-any)
Rcurvep_1.3.1.tar.gz(r-4.5-noble)Rcurvep_1.3.1.tar.gz(r-4.4-noble)
Rcurvep_1.3.1.tgz(r-4.4-emscripten)Rcurvep_1.3.1.tgz(r-4.3-emscripten)
Rcurvep.pdf |Rcurvep.html✨
Rcurvep/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/moggces/rcurvep/issues

Uses libs:
  • openjdk– OpenJDK Java runtime, using Hotspot JIT
Datasets:
  • zfishbeh - Subsets of concentration response datasets from zebrafish neurotoxicity assays
  • zfishdev - Subsets of concentration response datasets from zebrafish developmental toxicity assays
  • zfishdev_act - Activity output based on simulated datasets using zfishdev_all dataset
  • zfishdev_all - Full sets of concentration response datasets from zebrafish developmental toxicity assays

On CRAN:

14 exports 3 stars 1.33 score 47 dependencies 1 mentions 17 scripts 253 downloads

Last updated 8 months agofrom:6fa0b04819. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 07 2024
R-4.5-winOKSep 07 2024
R-4.5-linuxOKSep 07 2024
R-4.4-winOKSep 07 2024
R-4.4-macOKSep 07 2024
R-4.3-winOKSep 07 2024
R-4.3-macOKSep 07 2024

Exports:cal_knee_pointcombi_run_rcurvepcreate_datasetcurvepcurvep_defaultsestimate_dataset_bmrfit_cc2_modlfit_modlsget_hill_fit_configmerge_rcurvep_objsrun_fitrun_rcurvepsummarize_fit_outputsummarize_rcurvep_output

Dependencies:bootclicodetoolscolorspacecpp11digestdplyrfansifarverfurrrfuturegenericsggplot2globalsgluegtableisobandlabelinglatticelifecyclelistenvmagrittrMASSMatrixmgcvmunsellnlmeparallellypillarpkgconfigpurrrR6rbibutilsRColorBrewerRdpackrJavarlangscalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr

Parallel Computing Examples Using Rcurvep

Rendered fromfuture_rcurvep.Rmdusingknitr::rmarkdownon Sep 07 2024.

Last update: 2024-01-08
Started: 2024-01-08

Practical applications using Rcurvep package

Rendered frompractical_rcurvep.Rmdusingknitr::rmarkdownon Sep 07 2024.

Last update: 2023-12-23
Started: 2020-01-08