Package: quicR 2.1.0
quicR: RT-QuIC Data Formatting and Analysis
Designed for the curation and analysis of data generated from real-time quaking-induced conversion (RT-QuIC) assays first described by Atarashi et al. (2011) <doi:10.1038/nm.2294>. 'quicR' calculates useful metrics such as maxpoint ratio: Rowden et al. (2023) <doi:10.1099/vir.0.069906-0>; time-to-threshold: Shi et al. (2013) <doi:10.1186/2051-5960-1-44>; and maximum slope. Integration with the output from plate readers allows for seamless input of raw data into the R environment.
Authors:
quicR_2.1.0.tar.gz
quicR_2.1.0.zip(r-4.5)quicR_2.1.0.zip(r-4.4)quicR_2.1.0.zip(r-4.3)
quicR_2.1.0.tgz(r-4.5-any)quicR_2.1.0.tgz(r-4.4-any)quicR_2.1.0.tgz(r-4.3-any)
quicR_2.1.0.tar.gz(r-4.5-noble)quicR_2.1.0.tar.gz(r-4.4-noble)
quicR_2.1.0.tgz(r-4.4-emscripten)quicR_2.1.0.tgz(r-4.3-emscripten)
quicR.pdf |quicR.html✨
quicR/json (API)
NEWS
| # Install 'quicR' in R: |
| install.packages('quicR', repos = c('https://gage1145.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/gage1145/quicr/issues
Last updated 5 days agofrom:47e57c9134. Checks:5 OK, 3 NOTE. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 12 2025 |
| R-4.5-win | NOTE | Feb 12 2025 |
| R-4.5-mac | NOTE | Feb 12 2025 |
| R-4.5-linux | NOTE | Feb 12 2025 |
| R-4.4-win | OK | Feb 12 2025 |
| R-4.4-mac | OK | Feb 12 2025 |
| R-4.3-win | OK | Feb 12 2025 |
| R-4.3-mac | OK | Feb 12 2025 |
Exports:add_repsBMG_formatcalculate_metricscalculate_MPRcalculate_MScalculate_thresholdcalculate_TtTconvert_tablesget_metaget_realget_sample_locationsget_wellsnormalize_RFUorganize_tablesplate_viewplot_metricsseparate_rawtranspose_real
Dependencies:cellrangerclicolorspacecpp11crayondplyrfansifarvergenericsggplot2gluegtablehmsisobandjanitorlabelinglatticelifecyclelubridatemagrittrMASSMatrixmgcvmunsellnlmeopenxlsxpillarpkgconfigplyrprettyunitsprogresspurrrR6RColorBrewerRcppreadxlrematchreshape2rlangscalesslidersnakecasestringistringrtibbletidyrtidyselecttimechangeutf8vctrsviridisLitewarpwithrzip
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Add replicates | add_reps |
| Format Table for BMG Sample ID Import | BMG_format |
| Generate a dataframe with calculated metrics. | calculate_metrics |
| Calculate the Maxpoint Ratio | calculate_MPR |
| Calculate Maximum Slope | calculate_MS |
| Calculate a Threshold for Rate Determination | calculate_threshold |
| Calculate Time to Threshold | calculate_TtT |
| Convert tables into a single column in a dataframe. | convert_tables |
| Retrieve the BMG metadata | get_meta |
| Get Real-Time RT-QuIC Fluorescence Data | get_real |
| Get the well locations of the samples used in the RT-QuIC run. | get_sample_locations |
| Get the Wells Used in the RT-QuIC Run. | get_wells |
| Normalize Fluorescence | normalize_RFU |
| Organize MARS Tables | organize_tables |
| Real-Time Plate View | plate_view |
| Plot metrics generated from the "calculate" family of quicR functions. | plot_metrics |
| Separate Real-Time Data into separate dataframes. | separate_raw |
| Transpose Real-Time Data | transpose_real |
