Package: amplify 0.1.0

Kai Aragaki

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-4.6-any)
amplify_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
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

Pkgdown/docs site:https://kaiaragaki.github.io

Datasets:

dummy_rna_conc - Example data of RNA samples with concentrations

On CRAN:

1.70 score 5 scripts 19 exports 80 dependencies

Last updated from:d3bb78428f. Checks:7 FAIL, 1 ERROR, 1 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	FAIL	123
source / vignettes	ERROR	254
linux-release-x86_64	FAIL	139
macos-release-arm64	FAIL	86
macos-oldrel-arm64	FAIL	70
windows-devel	FAIL	83
windows-release	FAIL	90
windows-oldrel	FAIL	62
wasm-release	OK	138

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 commonmark cpp11 crayon curl digest doSNOW dplyr evaluate farver fastmap fontawesome forcats foreach fs generics ggplot2 glue gplate gt gtable highr hms htmltools htmlwidgets isoband iterators jquerylib jsonlite juicyjuice knitr labeling lifecycle litedown magrittr markdown memoise mime mop pillar pkgconfig prettyunits progress purrr R6 rappdirs RColorBrewer Rcpp reactable reactR readxl rematch rlang rmarkdown S7 sass scales snow stringi stringr terra tibble tidyr tidyselect tinytex utf8 V8 vctrs viridisLite withr xfun xml2 yaml

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

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