Changelog

Source: NEWS.md

NACHO 2.0.8

CRAN release: 2026-10-01

Bug Fixes

• In inst/app/,
  • fix: render the help pages from their text, so the app no longer writes to the installed package when R CMD check runs it.
  • fix: open the help pages of the quality-control metrics, whose links never matched their input names.
• In autoplot(),
  • fix: set the smoothing formula of the "PN" and "NORM" plots, which silences the ggplot2 geom_smooth() message.

NACHO 2.0.7

CRAN release: 2026-09-27

Dependencies

• In DESCRIPTION,
  • build: require R 4.1.0 or newer, ggplot2 4.0.0 or newer, ggforce 0.5.0 or newer, ggrepel 0.9.6 or newer, and shiny 1.7.4 or newer, which pulls in fontawesome 0.4.0 and its Font Awesome 6 icon names.
  • build: require pandoc 2.11 or newer, which has citeproc built in, so pandoc-citeproc is no longer needed.
  • build: require knitr 1.39 or newer, which the report needs for include_graphics(rel_path = FALSE).
  • build: require scales 1.4.0 or newer, which ggplot2 4.0.0 already needs, for the log-10 axes of the "PFNF" and "HF" plots.

Chores

• In inst/app/,
  • refactor: replace the superseded shiny::callModule() with shiny::moduleServer().
  • refactor: use the Font Awesome 6 icon names file-arrow-up and circle-info.
• In R/,
  • refactor: drop stringsAsFactors = FALSE from data.frame() and as.data.frame() calls, where it is the default since R 4.0.0.
  • refactor: hide boxplot outliers with outliers = FALSE instead of outlier.shape = NA.

Documentation

• In vignettes/, README.Rmd and the render() report template,
  • docs: write chunk options as #| YAML comments, which needs knitr 1.35 or newer.
  • docs: add alternative text to the images.
  • docs: install the development version with pak::pak() instead of remotes::install_github().
• docs: fix typos and grammar, and spell GitHub, NanoString, R Markdown and Shiny consistently.
• In vignettes/,
  • docs: keep only the GSE70970 samples measured with the NS_H_miR_1.4 CodeSet, since its two CodeSets come from different nSolver versions and load_rcc() refuses files that mix versions.
  • docs: attach data.table in the analysis vignette, which uses dcast() and as.data.table().
  • docs: link to GEO over https in the bibliography, since the http address now redirects.
• In pkgdown/,
  • docs: restyle the website for pkgdown 2.2 with the NACHO logo colours, a light and dark mode switch, and colour contrast that meets WCAG AA.
  • docs: group the reference index by task.
• In R/normalise.R, R/load_rcc.R and vignettes/NACHO.Rmd,
  • docs: remove the raw_counts and normalised_counts slots, which never existed, and say that nacho holds one row per sample and probe.
• In R/GSE74821.R,
  • docs: say that GSE74821 holds 48 samples, not 20.

Fixes

• In inst/CITATION,
  • fix: list the authors as person() objects, so the citation shows their full initials and spells Leen M. ’t Hart correctly.
  • fix: cite the version of record, Bioinformatics volume 36, issue 3, pages 970 to 971, published in February 2020.
• In R/autoplot.R,
  • fix: stop boxplots inheriting the colour aesthetic, which made ggplot2 warn that it dropped colour for the control probe plots.
  • fix: draw the outlier bands of the "PFNF" and "HF" plots to the panel edges without log-10 warnings about infinite values.
  • fix: keep each sample’s identifier in the "BD", "FoV", "PCL", "LoD", "PN", "Positive", "Negative" and "Housekeeping" plots, which drew every point at one position and dropped some of them.
• In R/render.R,
  • fix: include the logo by its absolute path, so pandoc finds it when the temporary directory sits behind a symbolic link.
  • fix: pass the report options as R Markdown parameters, so outliers_labels = "CartridgeID" works and column names with quotes no longer break the report.
• In inst/app/app.R,
  • fix: stop writing an all.rdata debug file to the working directory when uploading RCC files.
  • fix: load uploaded RCC files, which failed because suppressMessages() received x instead of expr.
  • fix: make the sample sheet optional again when uploading RCC files, instead of failing on a missing ssheet_dt.
• In DESCRIPTION,
  • fix: suggest markdown, which the app needs to show its help pages, and make visualise() ask for it when it is not installed. The deploy() help page notes that the server needs it too.
• In R/geometric_housekeeping.R,
  • fix: replace background-corrected housekeeping counts below 1 with 1, so values between 0 and 1 no longer inflate House_factor. (#53)
• In R/qc_pca.R,
  • fix: compute the PCA with samples as observations and store their scores. PC01 to PC10 and the variance explained change, and the PCA plots now show the main sources of variation between samples.
• In R/normalise_counts.R,
  • fix: apply the 0.1 floor after rounding, so normalised counts at or below background are 0.1 instead of 0. With housekeeping_predict = TRUE, the floor can change which housekeeping genes are picked, which in turn changes House_factor, the normalised counts and the outlier flags.
• In R/qc_pca.R and R/normalise_counts.R,
  • fix: objects created with an earlier version keep the old values, so run load_rcc() again to refresh them.
• In R/normalise.R,
  • fix: use the n_comp passed to normalise(), which was ignored.
  • fix: recompute is_outlier when only the thresholds change.
• In R/qc_features.R, R/qc_limit_detection.R and R/check_outliers.R,
  • fix: report PCL and LoD as NA when a panel has no POS_E probe or when the negative controls do not vary, and do not flag a sample on a metric that could not be measured.
• In R/load_rcc.R,
  • fix: detect PlexSet files from their content, and add plexset_id S1 to S8 when the sample sheet lists each file once.
  • fix: stop converting the caller’s sample sheet to a data.table.
  • fix: stop with a clear message when RCC files mix PlexSet and single-sample files.
  • fix: stop when a single-sample sample sheet lists the same RCC file twice.
• In R/print.R,
  • fix: return the object invisibly from print().
• In data/,
  • fix: rebuild GSE74821 with the corrected PCA and normalised counts.
• In inst/app/,
  • fix: set the full binding density range when switching between the MAX/FLEX and SPRINT presets.
  • fix: accept zip archives sent as application/zip, and .RCC, .rcc, .RCC.gz and .csv files in any case.
  • fix: stop warning about row names when unpacking a zip archive.
  • fix: show a notification when the sample sheet is discarded, instead of a warning in the R console.
  • fix: correct the typos in the card and outlier labels, and open the app on the QC metrics tab.

NACHO 2.0.6

CRAN release: 2024-01-12

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 highlight 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 R Markdown 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.