Changelog

Source: NEWS.md

NACHO 2.0.6

Fixes

• In R/qc_positive_control.R,
  • fix: use R-squared instead of Pearson correlation coefficient. (#48)

NACHO 2.0.5

CRAN release: 2023-08-07

Fixes

• In R/autoplot.R,
  • fix: set height in ggplot2::position_jitter() to 0 to avoid vertical dispersion points. (#45)
• In inst/app/www/about-nacho.md,
  • fix: shiny[dot]rstudio[dot]com moved to https://shiny.posit.co/.

Tests

• In tests/testthat/test-load_rcc.R,
  • fix: skip tests to decrease CRAN checks computation time.

Full Changelog: https://github.com/mcanouil/NACHO/compare/v2.0.4...v2.0.5

NACHO 2.0.4

CRAN release: 2023-04-01

Fixes

• In inst/CITATION,
  • fix: convert citEntry to bibentry from CRAN note.

Full Changelog: https://github.com/mcanouil/NACHO/compare/v2.0.3...v2.0.4

NACHO 2.0.3

Chores

• In DESCRIPTION,
  • chore: update domain name.

Full Changelog: https://github.com/mcanouil/NACHO/compare/v2.0.2...v2.0.3

NACHO 2.0.2

CRAN release: 2022-12-05

Chores

• In DESCRIPTION,
  • chore: update email address.
• chore: remove ggbeeswarm.

Full Changelog: https://github.com/mcanouil/NACHO/compare/v2.0.1...v2.0.2

NACHO 2.0.1

CRAN release: 2022-11-24

Chores

• In DESCRIPTION,
  • chore: update email address.

Full Changelog: https://github.com/mcanouil/NACHO/compare/v2.0.0...v2.0.1

NACHO 2.0.0

CRAN release: 2022-05-31

Major (breaking) changes

• Refactor to use data.table instead of dplyr/tidyr/purrr.

Features

• Ensure RCC files are homogeneous in terms of versions. #20
• Allow to use vector of file paths, named or not. #33
• Allow to upload a CSV file associated with the RCC files within the shiny application. #36

Full Changelog: https://github.com/mcanouil/NACHO/compare/v1.1.0...v2.0.0

NACHO 1.1.0

CRAN release: 2021-01-14

Breaking changes

• In DESCRIPTION,
  • Update ggplot2 version (>= 3.3.0).
  • Update dplyr version (>= 1.0.2).
• In R/autoplot.R,
  • Replace ggplot2::expand_scale() with ggplot2::expansion().

Minor improvements and fixes

• In R/load_rcc.R,
  • Remove deprecated dplyr::progress_estimated().
• In R/norm_glm.R,
  • Remove deprecated dplyr::progress_estimated().
• In tests,
  • Small tweaks.
  • Add condition when trying to download files from a GEO dataset (Fix CRAN checks).

NACHO 1.0.2

CRAN release: 2021-01-05

Minor improvements and fixes

• In DESCRIPTION,
  • Update URLs.
• In R/normalise.R,
  • Fix missing “outliers_thresholds” field after normalise() without removing outliers (#26).
• In R/GSE74821.R,
  • Now uses data-raw root directory.
• In R/-,
  • No longer generates Rd files for internal functions.

NACHO 1.0.1

CRAN release: 2020-05-26

Minor improvements and fixes

• Fix deprecated documentation for R/load_rcc.R and R/normalise.R.
• Use file.path() in examples and vignette.
• In R/autoplot.R, reduce alpha for ellipses.
• In inst/app/utils.R, set default point size (also for outliers) to 1.
• In R/load_rcc.R, use inherits() instead of class().
• Code optimisation.

NACHO 1.0.0

CRAN release: 2020-01-09

New features

• In R/conflicts.R,
  • conflicts are now printed when attaching NACHO.
  • nacho_conflicts() can be used to print conflicts.
• New Shiny app in inst/app/, (#4, #5 & #14)
  • as a regular app, to load directly RCC files individually or within zip archive.
  • within visualise(), to load "nacho" object from load_rcc() (previous summarise()) or from normalise().
• New deploy() (R/deploy.R) function to easily deploy (copy) the shiny app.
• New raw RCC files (multiplexed) available in inst/extdata/.
• New vignette NACHO-analysis, which describe how to use limma or other model after using –NACHO–.
• In DESCRIPTION,
  • Order packages in alphabetical order.
  • Add packages’ version.

Breaking changes

• summarise() and summarize() have been deprecated and replaced with load_rcc(). (#12 & #15)
• Counts matrices (raw_counts and normalised_counts) are no longer (directly) available, -i.e.-, counts are available in a long format within the nacho slot of a nacho object.
• visualise(), now uses a new shiny app (inst/app/).

Minor improvements and fixes

• In R/visualise.R, R/render.R, print(), R/load_rcc.R and R/normalise.R,
  • replace function to check for outliers, now uses check_outliers().
• In R/visualise.R, replace datatable (render and output) with classical table. (#13)
• In R/autoplot.R,
  • add show_outliers to show outliers differently on plots (-i.e.-, in red).
  • add outliers_factor to highligth outliers with different point size.
  • add outliers_labels to print labels on top of outliers.
  • now uses tidyeval via import.
  • remove plexset ID (_S-) to remove duplicated QC metrics.
• In R/print.R, now print a table with outliers if any (with echo = TRUE).
• In R/GSE74821.R, dataset is up to date according to NACHO functions.

NACHO 0.6.1

CRAN release: 2019-10-12

Minor improvements and fixes

• In DESCRIPTION, add "SystemRequirements: pandoc (>= 1.12.3) - http://pandoc.org, pandoc-citeproc".
• In R/render.R,
  • explicit import for opts_chunk::knitr in roxygen documentation.
  • explicit import for sessioninfo::session_info in roxygen documentation.
• In tests/testthat/test-render.R, now checks if pandoc is available.
• In tests/testthat/test-summarise.R, fix tests when connection to GEO is alternatively up/down between two tests.

NACHO 0.6.0

CRAN release: 2019-10-07

Citation

• Add citation (#8).

New features

• autoplot() allows to plot a chosen QC plot available in the shiny app (visualise()) and/or in the HTML report (render()).
• print() allows to print the structure or to print text and figures formatted using markdown (mainly to be used in a Rmakrdown chunk).
• render() render figures from visualise() in a HTML friendly output.

Minor improvements and fixes

• In R/read_rcc.R, R/summarise.R,
  • fix issue (#1) when PlexSet RCC files could not be read.
  • update code to use tidyr 1.0.0 (#9).
• In R/summarise.R,
  • object returned is of S3 class “nacho” for ease of use of autoplot().
  • update code to use tidyr 1.0.0 (#9).
• In R/normalise.R,
  • object returned is of S3 class “nacho” for ease of use of autoplot().
  • fix missing outliers_thresholds component in returned object.
• In R/visualise.R,
  • minor code changes.
  • return app object in non-interactive session.
• In vignettes/NACHO.Rmd,
  • fix several typos.
  • add sections for autoplot(), print() and render() (#7).
  • fix chunk output (-i.e.-, remove default results = "asis").
  • fix normalise() call with custom housekeeping genes (-i.e.-, set housekeeping_predict = FALSE) (#10).

NACHO 0.5.6

CRAN release: 2019-04-29

Minor improvements and fixes

• In tests/testthat/test-summarise.R, add condition to handle when GEOQuery is down and cannot retrieve online data.
• In vignettes/NACHO.Rmd, add condition to handle when GEOQuery is down and cannot retrieve online data.

NACHO 0.5.5

CRAN release: 2019-04-28

Minor improvements and fixes

• In R/summarise.R, put example in if (interactive()) {...} instead of \dontrun{...}.
• In R/normalise.R, put example in if (interactive()) {...} instead of \dontrun{...}.
• In R/visualise.R, put example in if (interactive()) {...} instead of \dontrun{...}.
• In DESCRIPTION and README, description updated for CRAN, by adding “messenger-RNA/micro-RNA”.

NACHO 0.5.4

Minor improvements and fixes

• In R/normalise.R, add short running example for normalise().
• In R/visualise.R, add short running example for visualise().
• In DESCRIPTION, description updated for CRAN, by removing some capital letters and put –NACHO– between single quotes.

NACHO 0.5.3

Minor improvements and fixes

• Bold letters for –NACHO– in title.
• In DESCRIPTION, title and description updated for CRAN.
• Add NanoString reference in DESCRIPTION and vignette

NACHO 0.5.2

Minor improvements and fixes

• In DESCRIPTION, title and description updated for CRAN.

NACHO 0.5.1

Minor improvements and fixes

• Vignette uses bib file for references.
• Update URL in DESCRIPTION.

NACHO 0.5.0

New features

• summarise() imports and pre-process RCC files.
• normalise() allows to change settings used in summarise() and exclude outliers.
• visualise() allows customisation of the quality thresholds.
• Minor changes

Minor improvements and fixes

• Add a README.
• Add logo.
• In summarise(), ssheet_csv can take a data.frame or a csv file.
• Change in package title with capital letters corresponding to NACHO.
• Add tests using testthat.

NACHO 0.4.0

• Fix major errors, bad behaviour and typos.

NACHO 0.3.1

• Add and fill roxygen documentation.

NACHO 0.3.0

• Code optimisation in normalise() (and internal functions).
• visualise() replaces the Shiny app.

NACHO 0.2.2

• Remove S4 class => Back to list object.

NACHO 0.2.1

• Rewrite GEO dataset.

NACHO 0.2.0

• Complete rewrite of summarise() and normalise() (and all internal functions).
• Add S4 class object.

NACHO 0.1.0

• First version.