Title: Real-Time PCR Data Sets by Boggy et al. (2010)
Version: 0.0.1
Description: Real-time quantitative polymerase chain reaction (qPCR) data sets by Boggy et al. (2008) <doi:10.1371/journal.pone.0012355>. This package provides a dilution series for one PCR target: a random sequence that minimizes secondary structure and off-target primer binding. The data set is a six-point, ten-fold dilution series. For each concentration there are two replicates. Each amplification curve is 40 cycles long. Original raw data file: https://journals.plos.org/plosone/article/file?type=supplementary&id=10.1371/journal.pone.0012355.s004.
License: CC BY 4.0
Encoding: UTF-8
RoxygenNote: 7.3.1
Imports: tibble
Depends: R (≥ 2.10)
LazyData: true
URL: https://rmagno.eu/boggy/, https://github.com/ramiromagno/boggy
BugReports: https://github.com/ramiromagno/boggy/issues
NeedsCompilation: no
Packaged: 2024-04-24 15:41:49 UTC; rmagno
Author: Ramiro Magno ORCID iD [aut, cre], Pattern Institute [cph, fnd]
Maintainer: Ramiro Magno <rmagno@pattern.institute>
Repository: CRAN
Date/Publication: 2024-04-25 16:10:02 UTC

boggy: Real-Time PCR Data Sets by Boggy et al. (2010)

Description

Real-time quantitative polymerase chain reaction (qPCR) data sets by Boggy et al. (2008) doi:10.1371/journal.pone.0012355. This package provides a dilution series for one PCR target: a random sequence that minimizes secondary structure and off-target primer binding. The data set is a six-point, ten-fold dilution series. For each concentration there are two replicates. Each amplification curve is 40 cycles long. Original raw data file: https://journals.plos.org/plosone/article/file?type=supplementary&id=10.1371/journal.pone.0012355.s004.

Author(s)

Maintainer: Ramiro Magno rmagno@pattern.institute (ORCID)

Other contributors:

See Also

Useful links:

qPCR data set by Boggy et al. (2010)

Description

The qPCR data set named s1 comprises a six-point, ten-fold dilution series, replicated in duplicates targeting an amplicon designed with a random sequence that minimizes secondary structure and off-target primer binding. Please read the Quantitative PCR data section, qPCR assays subsection of Boggy et al. (2010) for more details.

Format

A tibble with 480 rows and 10 variables:

plate

Plate identifier. For this data set it is always missing (NA).

well

Well identifier.

dye

The type of dye used. In this data set the values are always "SYTO 13", meaning 2 mM of the dsDNA dye SYTO-13 (Invitrogen, Carlsbad, CA).

target

Target identifier: the amplicon used, a random sequence dubbed "S1" by the original authors.

sample_type

Sample type (all curves are standards, i.e. "std").

replicate

Replicate identifier: either 1 or 2.

copies

Standard copy number.

dilution

Dilution factor. Higher number means greater dilution.

cycle

PCR cycle.

fluor

Raw fluorescence values.

Source

doi:10.1371/journal.pone.0012355

Examples

s1