tidyqpcr - v1.0.0

v1.0.0 is the release of tidyqpcr after software review and acceptance by rOpenSci.

• removed plot_helper functions https://github.com/ropensci/tidyqpcr/commit/36a16f67335ab8d3890fc4945dcde5d097f347ff
• explicitly use the "by" argument in all joins, updated tests https://github.com/ropensci/tidyqpcr/commit/d010f66922892b6024c81c03606e99a662d68708
• cleaned up tests https://github.com/ropensci/tidyqpcr/commit/a113a9a9e3fc00376da711e44e995b71797d4f39
• fixed urls in README.md https://github.com/ropensci/tidyqpcr/commit/60b354f54092a140781aa166ea1cb9ecb2cd31f0
• updates to transfer ownership to rOpenSci, including
  • changing all links to point to https://github.com/ropensci/tidyqpcr/ https://github.com/ropensci/tidyqpcr/commit/b6b0f2a28c3e031f690a77fd84726890ad2f3665
  • updating peer review badge, author formatting, fixing dois in the paper, other minor formatting edits

Scientific Software - Peer-reviewed - R
Published by ewallace about 4 years ago

tidyqpcr - v0.5

Updates to v0.5 in response to rOpenSci review 2nd round. Mostly improvements in documentation and help files, and a change to display_plate functions to make more general and more specialised versions.

• Added missing files to .Rbuildignore and changed references to licence, version and depends in DESCRIPTION https://github.com/ewallace/tidyqpcr/commit/fa29569fcee2769dcfb14526a843aadafdf6f1ba
• made packages explicit in tests https://github.com/ewallace/tidyqpcr/commit/d31933b59542593ddf372b0a12656bc14c95041c
• getting started moved in readme c05f925b1b8f0b4f2295cea165f646cb9d490a5d
• Added top-level help-file 98f930b7143c2dec68ba2e52e71706103f39b501
• Adds readqpcrdata.R tests f5816f1858607b1ec512edff5c56563c4fb52508
• Removes {lifecycle} from description da45200631965af2b402a1b22bcdf398460d1007
• Address spelling errors cfe2e7c5c509853b1d10e9788f94a4a20bcec3d6 and 8f354b5743849f3c6f47068b9e1c79cbb91d3cdb
• calculatedydx1 to calculate_dydx 45649a114b1878951e5fea036b3d9d1b34c5d359
• changes labelplaterowcol warnings to notes ba1eb67493c594f249bdf6c4d8306943f1c7103b
• changes displayplateqpcr() to enable displayplate() to be more general bd482f225bd77a58ab2bb5fd73bb7a8a4a5ec3fd. Older code will need to use displayplateqpcr to ensure that sampleid and target_id info displays.
• improved plot_helpers.R styling 55f4ca5104b2b64394d685a938a9f9f5f32384e6
• Adds basic usage to the Readme 25bed2de902f5a095354699a2253988b76667bf5
• Updates pkgdown website b88ed9f66e399c56dcc2771f4fb955f923fc7841

Scientific Software - Peer-reviewed - R
Published by ewallace about 4 years ago

tidyqpcr - Checks, documentation, vignettes, for rOpenSci resubmission

Many improvements, mostly to documentation and vignettes. This release was prepared for resubmission to rOpenSci software review

• Echo setup code chunk in vignettes #137
• Documentation for plate setup avoiding edge wells #132
• Visualizing measurement results in the plate layout in calibration vignette #131
• Fix vignette titles #130
• Reduce package footprint below 5MB by compressing data #128
• Rewrite description of other packages #126
• Tabulate MIQE requirements addressed by tidyqpcr and other R packages #125
• Improved Function documentation #124
• Vignette packages and files, use system.file and explain it #122, #145
• Clarify README #121
• Remove deprecated getdRdTall #103
• Document multi-plate calculations and validate inputs of calculatedrdtplate #104

Scientific Software - Peer-reviewed - R
Published by ewallace over 4 years ago

tidyqpcr - Stable version with tests for rOpenSci submission

• Includes tests with 80% code coverage
• Examples for every function
• Improved README with status badges
• JOSS-format paper.md draft
• Submitted to rOpensci for software review

Scientific Software - Peer-reviewed - R
Published by ewallace over 4 years ago

tidyqpcr - bug & documentation fixes in relative quantification

Scientific Software - Peer-reviewed - R
Published by ewallace over 5 years ago

tidyqpcr - relative quantification with delta Cq and delta delta Cq

Upgraded features for relative quantification, new vignettes to explain these, and gave functions more helpful names such as calculate... as well as create...

• lay out and display 96/384-well plates for easy experimental setup (label_plate_rowcol, create_blank_plate, ...)
• read-in Cq and raw data from Roche LightCycler machines with single-channel fluorescence (read_lightcycler_1colour_cq, read_lightcycler_1colour_raw)
• delta Cq: normalization/ relative quantification of Cq data to one or more reference targets by delta count method (calculate_normcq, calculate_deltacq_bysampleid)
• delta delta Cq: normalization of delta Cq data across multiple samples (calculate_deltadeltacq_bytargetid)
• calibration of primer sets including estimating efficiencies and visualization of curves (calculate_efficiency, and see vignettes)
• visualization of amplification and melt curves (calculate_drdt_plate, and see vignettes)

Scientific Software - Peer-reviewed - R
Published by ewallace almost 6 years ago

tidyqpcr - version 0.1 alpha with Sample, Probe, Ct

Code that used tidyqpcr before April 2020 should work using this release. The required variables for a plate plan analysis were: * Sample (later replaced by SampleID) * Probe (later replaced by TargetID) * Type (still there) * Ct (later replaced

We packaged this into a release to enable users to re-run old analysis scripts without rewriting.

Scientific Software - Peer-reviewed - R
Published by ewallace about 6 years ago