Package: amplify 0.1.0

amplify: Automate PCR Tasks Reproducibly

PCR tasks - like plate layout planning, dilution calculations, visualization, and analysis - are often repetitive, tedious, prone to error, and poorly documented. amplify seeks to automate these tasks, as well as documenting them (through both code and generated reports) as a bonus.

Authors:Kai Aragaki [aut, cre]

amplify_0.1.0.tar.gz

amplify_0.1.0.tar.gz(r-4.4-noble)
amplify_0.1.0.tgz(r-4.4-emscripten)amplify_0.1.0.tgz(r-4.3-emscripten)
amplify.pdf |amplify.html✨
amplify/json (API)

# Install 'amplify' in R:

install.packages('amplify', repos = c('https://kaiaragaki.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/kaiaragaki/amplify/issues

Datasets:

dummy_rna_conc - Example data of RNA samples with concentrations

On CRAN:

3.78 score 4 scripts 19 exports 86 dependencies

Last updated 2 months agofrom:d3bb78428f. Checks:OK: 1. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 05 2024

Exports:as_pcr pcr_calc_slope pcr_control pcr_lib_calc pcr_lib_qc pcr_lib_qc_plot_conc pcr_lib_qc_plot_dil pcr_lib_qc_plot_outliers pcr_lib_qc_plot_slope pcr_lib_qc_report pcr_plan pcr_plan_report pcr_plate_view pcr_plot pcr_rq read_pcr scrub tidy_lab well_data

Dependencies:base64enc bigD bitops bslib cachem cellranger cli codetools colorspace commonmark cpp11 crayon curl digest doSNOW dplyr evaluate fansi farver fastmap fontawesome forcats foreach fs generics ggplot2 glue gplate gt gtable highr hms htmltools htmlwidgets isoband iterators jquerylib jsonlite juicyjuice knitr labeling lattice lifecycle magrittr markdown MASS Matrix memoise mgcv mime mop munsell nlme pillar pkgconfig prettyunits progress purrr R6 rappdirs RColorBrewer Rcpp reactable reactR readxl rematch rlang rmarkdown sass scales snow stringi stringr terra tibble tidyr tidyselect tinytex utf8 V8 vctrs viridisLite withr xfun xml2 yaml

Analyzing ddCt qPCR with amplify

Rendered fromanalyzing-ddctqrtpcr.Rmdusingknitr::rmarkdownon Nov 05 2024.

Last update: 2024-10-05
Started: 2021-10-13

Performing Library Quantification QC

Rendered fromperforming-lib-quant-qc.Rmdusingknitr::rmarkdownon Nov 05 2024.

Last update: 2024-10-04
Started: 2021-10-17

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Example data of RNA samples with concentrations	dummy_rna_conc
Recalcuate standard slope of quantity vs Ct	pcr_calc_slope
Calculate Delta Ct mean based on given control probe	pcr_control pcr_control.data.frame pcr_control.pcr
Calculate library PCR concentrations	pcr_lib_calc
Create library prep quality control data	pcr_lib_qc
Plot concentration of libraries across samples	pcr_lib_qc_plot_conc
Plot standard dilutions compared to a perfect dilution	pcr_lib_qc_plot_dil
Plot mean centered samples without putative outliers	pcr_lib_qc_plot_outliers
Plot the log of library quantities vs Ct	pcr_lib_qc_plot_slope
Generate visual library prep pcr quality control report	pcr_lib_qc_report
Plan PCR experiment	pcr_plan
Create a report from a PCR plan	pcr_plan_report
View sample plating layout	pcr_plate_view
Plot qPCR results	pcr_plot pcr_plot.data.frame pcr_plot.pcr
Recalculate relative quantities for a given experiment	pcr_rq pcr_rq.data.frame pcr_rq.pcr