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NACHO (development version)

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

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,

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

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

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

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

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

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

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

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

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

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

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

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

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.