Changes in version 2.0.6.9000 Changes in version 2.0.6 (2024-01-12) Fixes - In R/qc_positive_control.R, - fix: use R-squared instead of Pearson correlation coefficient. (#48) Changes in version 2.0.5 (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 Changes in version 2.0.4 (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 Changes in version 2.0.3 Chores - In DESCRIPTION, - chore: update domain name. Full Changelog: https://github.com/mcanouil/NACHO/compare/v2.0.2...v2.0.3 Changes in version 2.0.2 (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 Changes in version 2.0.1 (2022-11-24) Chores - In DESCRIPTION, - chore: update email address. Full Changelog: https://github.com/mcanouil/NACHO/compare/v2.0.0...v2.0.1 Changes in version 2.0.0 (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 Changes in version 1.1.0 (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). Changes in version 1.0.2 (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. Changes in version 1.0.1 (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. Changes in version 1.0.0 (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. Changes in version 0.6.1 (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. Changes in version 0.6.0 (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). Changes in version 0.5.6 (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. Changes in version 0.5.5 (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". Changes in version 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. Changes in version 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 Changes in version 0.5.2 Minor improvements and fixes - In DESCRIPTION, title and description updated for CRAN. Changes in version 0.5.1 Minor improvements and fixes - Vignette uses bib file for references. - Update URL in DESCRIPTION. Changes in version 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. Changes in version 0.4.0 - Fix major errors, bad behaviour and typos. Changes in version 0.3.1 - Add and fill roxygen documentation. Changes in version 0.3.0 - Code optimisation in normalise() (and internal functions). - visualise() replaces the Shiny app. Changes in version 0.2.2 - Remove S4 class => Back to list object. Changes in version 0.2.1 - Rewrite GEO dataset. Changes in version 0.2.0 - Complete rewrite of summarise() and normalise() (and all internal functions). - Add S4 class object. Changes in version 0.1.0 - First version.