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,
  • fix: shiny[dot]rstudio[dot]com moved to https://shiny.posit.co/.

Tests

• In tests/testthat/test-load_rcc.R,
  • fix: add testthat::skip_on_cran() to decrease CRAN checks computation time.

Full Changelog: v2.0.4...v2.0.5

NACHO 2.0.4

Fixes

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

Full Changelog: v2.0.3...v2.0.4

NACHO 2.0.3

Chores

• In DESCRIPTION,
  • chore: update domain name.

Full Changelog: v2.0.2...v2.0.3

NACHO 2.0.2

Chores

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

Full Changelog: v2.0.1...v2.0.2

NACHO 2.0.1

Chores

• In DESCRIPTION,
  • chore: update email address.

Full Changelog: 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: 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.