Package: QuICSeedR 0.1.2
Manci Li
QuICSeedR: Analyze Data for Fluorophore-Assisted Seed Amplification Assays
A toolkit for analysis and visualization of data from fluorophore-assisted seed amplification assays, such as Real-Time Quaking-Induced Conversion (RT-QuIC) and Fluorophore-Assisted Protein Misfolding Cyclic Amplification (PMCA). 'QuICSeedR' addresses limitations in existing software by automating data processing, supporting large-scale analysis, and enabling comparative studies of analysis methods. It incorporates methods described in Henderson et al. (2015) <doi:10.1099/vir.0.069906-0>, Li et al. (2020) <doi:10.1038/s41598-021-96127-8>, Rowden et al. (2023) <doi:10.3390/pathogens12020309>, Haley et al. (2013) <doi:10.1371/journal.pone.0081488>, and Mair and Wilcox (2020) <doi:10.3758/s13428-019-01246-w>. Please refer to the original publications for details.
Authors:
QuICSeedR_0.1.2.tar.gz
QuICSeedR_0.1.2.tar.gz(r-4.5-noble)QuICSeedR_0.1.2.tar.gz(r-4.4-noble)
QuICSeedR_0.1.2.tgz(r-4.4-emscripten)QuICSeedR_0.1.2.tgz(r-4.3-emscripten)
QuICSeedR.pdf |QuICSeedR.html✨
QuICSeedR/json (API)
| # Install 'QuICSeedR' in R: |
| install.packages('QuICSeedR', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 3 months agofrom:db2768448e. Checks:OK: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 02 2024 |
| R-4.5-linux | OK | Nov 02 2024 |
Exports:BulkProcessingBulkReadMARSCleanMetaCleanRawConvertTimeGetAnalysisGetCalculationGetReplicatePlotMetricPlotPlatePlotRawMultiPlotRawSingleSpreadCalculationSummarizeResult
Dependencies:cellrangerclicolorspacecpp11crayondplyrfansifarvergenericsggplot2gluegtablehmsisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigplyrprettyunitsprogresspurrrR6RColorBrewerRcppreadxlrematchreshaperlangscalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithrWRS2
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Processing and analyzing Multiple Experiments | BulkProcessing |
| Bulk Read MARS data | BulkReadMARS |
| Get Clean Metadata | CleanMeta |
| Generate Clean Raw Data | CleanRaw |
| Extract and Convert Time Data to Decimal Hours | ConvertTime |
| Perform Statistical Analysis on Calculations | GetAnalysis |
| Perform Calculations | GetCalculation |
| Generate Replicate Numbers for Plate Data | GetReplicate |
| Create a customizable ggplot for metrics | PlotMetric |
| Plot Time Series Data | PlotPlate |
| Plot Multiple Samples from the Cleaned Raw Data | PlotRawMulti |
| Plot a Single Sample from the Cleaned Raw Data | PlotRawSingle |
| Spread Calculation Data | SpreadCalculation |
| Summarize Analysis Results | SummarizeResult |