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).
| Version: | 1.3.1 |
| Depends: | R (≥ 3.5) |
| Imports: | dplyr (≥ 1.0.0), tibble, magrittr, tidyselect, boot, tidyr, purrr, rlang, stringr, ggplot2, Rdpack, methods, rJava, furrr |
| Suggests: | testthat, knitr, rmarkdown, tcpl, future |
| Published: | 2024-01-09 |
| Author: | Jui-Hua Hsieh 
[aut, cre],
Alexander Sedykh [aut],
Fred Parham [ctb],
Yuhong Wang [ctb],
Tongan Zhao [aut],
Ruili Huang [ctb] |
| Maintainer: | Jui-Hua Hsieh <juihua.hsieh at gmail.com> |
| BugReports: | https://github.com/moggces/Rcurvep/issues |
| License: | MIT + file LICENSE |
| URL: | https://github.com/moggces/Rcurvep |
| NeedsCompilation: | no |
| SystemRequirements: | Java |
| Language: | en-US |
| Materials: | README NEWS |
| CRAN checks: | Rcurvep results |
Documentation:
| Reference manual: | Rcurvep.pdf |
| Vignettes: |
Parallel Computing Examples Using Rcurvep Practical applications using Rcurvep package |
Downloads:
| Package source: | Rcurvep_1.3.1.tar.gz |
| Windows binaries: | r-devel: Rcurvep_1.3.1.zip, r-release: Rcurvep_1.3.1.zip, r-oldrel: Rcurvep_1.3.1.zip |
| macOS binaries: | r-release (arm64): Rcurvep_1.3.1.tgz, r-oldrel (arm64): Rcurvep_1.3.1.tgz, r-release (x86_64): Rcurvep_1.3.1.tgz, r-oldrel (x86_64): Rcurvep_1.3.1.tgz |
| Old sources: | Rcurvep archive |
Linking:
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