Package: tidyqpcr 1.0

Edward Wallace

tidyqpcr: Quantitative PCR Analysis with the Tidyverse

For reproducible quantitative PCR (qPCR) analysis building on packages from the ’tidyverse’, notably ’dplyr’ and ’ggplot2’. It normalizes (by ddCq), summarizes, and plots pre-calculated Cq data, and plots raw amplification and melt curves from Roche Lightcycler (tm) machines. It does NOT (yet) calculate Cq data from amplification curves.

Authors:Edward Wallace [aut, cre], Sam Haynes [aut]

tidyqpcr_1.0.tar.gz
tidyqpcr_1.0.zip(r-4.5)tidyqpcr_1.0.zip(r-4.4)tidyqpcr_1.0.zip(r-4.3)
tidyqpcr_1.0.tgz(r-4.4-any)tidyqpcr_1.0.tgz(r-4.3-any)
tidyqpcr_1.0.tar.gz(r-4.5-noble)tidyqpcr_1.0.tar.gz(r-4.4-noble)
tidyqpcr_1.0.tgz(r-4.4-emscripten)tidyqpcr_1.0.tgz(r-4.3-emscripten)
tidyqpcr.pdf |tidyqpcr.html✨
tidyqpcr/json (API)

# Install 'tidyqpcr' in R:
install.packages('tidyqpcr', repos = c('https://ropensci.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/ropensci/tidyqpcr/issues

On CRAN:

miqeqpcrqpcr-analysistidyverse

24 exports 45 stars 2.86 score 48 dependencies

Last updated 3 months agofrom:0d3f62f16c (on main)

Exports:calculate_deltacq_bysampleidcalculate_deltadeltacq_bytargetidcalculate_drdt_platecalculate_dydxcalculate_efficiencycalculate_efficiency_bytargetidcalculate_normvaluecreate_blank_platecreate_blank_plate_1536wellcreate_blank_plate_96wellcreate_colkey_4diln_2ctrl_in_24create_colkey_6_in_24create_colkey_6diln_2ctrl_in_24create_rowkey_4_in_16create_rowkey_8_in_16_plaindebaselinedisplay_platedisplay_plate_qpcrdisplay_plate_valuelabel_plate_rowcolmake_row_names_echo1536make_row_names_lc1536read_lightcycler_1colour_cqread_lightcycler_1colour_raw

Dependencies:assertthatbitbit64clicliprcolorspacecpp11crayondplyrfansifarverforcatsgenericsggplot2gluegtablehmsisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigprettyunitsprogresspurrrR6RColorBrewerreadrrlangscalesstringistringrtibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithr

Delta Cq 96-well plate qPCR analysis example

Stuart McKellar and Edward Wallace

Rendered fromdeltacq_96well_vignette.Rmdusingknitr::rmarkdownon Jun 28 2024.

Last update: 2022-06-08
Started: 2020-09-04

Introduction to designing an experiment and setting up a plate plan in tidyqpcr

Edward Wallace

Rendered fromplatesetup_vignette.Rmdusingknitr::rmarkdownon Jun 28 2024.

Last update: 2022-06-08
Started: 2020-03-15

Multifactorial multi-plate qPCR analysis example

Edward Wallace

Rendered frommultifactor_vignette.Rmdusingknitr::rmarkdownon Jun 28 2024.

Last update: 2022-06-08
Started: 2019-09-25

Primers and probes calibration vignette

Edward Wallace

Rendered fromcalibration_vignette.Rmdusingknitr::rmarkdownon Jun 28 2024.

Last update: 2022-06-08
Started: 2019-09-25

Readme and manuals

Help Manual

Help pageTopics
Calculate delta cq (Delta Cq) to normalize quantification cycle (log2-fold) data within sample_id.calculate_deltacq_bysampleid
Calculate delta delta cq (Delta Delta Cq) to globally normalize quantification cycle (log2-fold) data across sample_id.calculate_deltadeltacq_bytargetid
Calculate dR/dT of melt curves for of every well in a plate.calculate_drdt_plate
Calculate dy/dx vector from vectors y and xcalculate_dydx
Calibrate primer sets / probes by calculating detection efficiency and R squaredcalculate_efficiency
Calibrate multiple probes by calculating detection efficiency and R squaredcalculate_efficiency_bytargetid
Calculate a normalized value for a subset of reference idscalculate_normvalue
Create a blank plate template as a tibble (with helper functions for common plate sizes)create_blank_plate create_blank_plate_1536well create_blank_plate_96well
Create a 4-dilution column key for primer calibrationcreate_colkey_4diln_2ctrl_in_24
Create a 6-value, 24-column key for platescreate_colkey_6_in_24
Create a 6-dilution column key for primer calibrationcreate_colkey_6diln_2ctrl_in_24
Create a 4-value, 16-row key for platescreate_rowkey_4_in_16
Create a plain 8-value, 16-row key for platescreate_rowkey_8_in_16_plain
Remove baseline from amplification curves (BETA)debaseline
Display an empty plate plan which can be populated with ggplot2 geom elements.display_plate
Display qPCR plate plan with sample_id, target_id, prep_type per welldisplay_plate_qpcr
Display the value of each well across the plate.display_plate_value
Label a plate with sample and probe informationlabel_plate_rowcol
Generates row names for the Labcyte Echo 1536-well platesmake_row_names_echo1536
Generates row names for the Roche Lightcycler (tm) 1536-well platesmake_row_names_lc1536
Reads quantification cycle (cq) data in 1 colour from Roche Lightcyclersread_lightcycler_1colour_cq
Reads raw text-format fluorescence data in 1 colour from Roche Lightcyclersread_lightcycler_1colour_raw