Function reference • amplify

Reading in Data

One-stop-shop for reading in and tidying PCR result files

pcr_tidy(): Tidy a PCR Excel File

Visualizing the Plate

Functions to visualize a variable - like Ct or sample name - as though you were looking at the plate

pcr_plate_view(): View sample plating layout

Comparative (ddCT) qPCR

Functions to calculate relative quantities, reset control samples/genes, plot data, plan experiments, etc.

pcr_plan(): Plan PCR experiment

pcr_plan_report(): Create a report from a PCR plan

pcr_plot(): Plot qPCR results

pcr_control(): (Re)calculate Delta Ct mean based on given control probe

pcr_rq(): (Re)calculate rq for a given sample

Standard Curve qPCR

Functions to calculate concentrations as well as assess quality of standard curve and efficiency.

pcr_lib_calc(): Calculate library PCR concentrations

pcr_lib_qc(): Create library prep quality control data

pcr_lib_qc_plot_conc(): Plot concentration of libraries across samples

pcr_lib_qc_plot_dil(): Plot standard dilutions compared to a perfect dilution

pcr_lib_qc_plot_outliers(): Plot mean centered samples without putative outliers

pcr_lib_qc_plot_slope(): Plot the log of library quantities vs Ct

pcr_lib_qc_report(): Generate visual library prep pcr quality control report

pcr_calc_slope(): Recalcuate standard slope of quantity vs Ct

Miscellaneous

Miscellaneous Utilities

pad_zero(): Add leading 0 to sample names

dummy_rna_conc: Example data of RNA samples with concentrations