R/qc_positive_control.R,
R/autoplot.R,
height in ggplot2::position_jitter() to 0 to avoid vertical dispersion points. (#45)inst/app/www/about-nacho.md,
tests/testthat/test-load_rcc.R,
Full Changelog: https://github.com/mcanouil/NACHO/compare/v2.0.4...v2.0.5
inst/CITATION,
citEntry to bibentry from CRAN note.Full Changelog: https://github.com/mcanouil/NACHO/compare/v2.0.3...v2.0.4
DESCRIPTION,
Full Changelog: https://github.com/mcanouil/NACHO/compare/v2.0.2...v2.0.3
DESCRIPTION,
ggbeeswarm.Full Changelog: https://github.com/mcanouil/NACHO/compare/v2.0.1...v2.0.2
DESCRIPTION,
Full Changelog: https://github.com/mcanouil/NACHO/compare/v2.0.0...v2.0.1
data.table instead of dplyr/tidyr/purrr.shiny application. #36Full Changelog: https://github.com/mcanouil/NACHO/compare/v1.1.0...v2.0.0
DESCRIPTION,
ggplot2 version (>= 3.3.0).dplyr version (>= 1.0.2).R/autoplot.R,
ggplot2::expand_scale() with ggplot2::expansion().R/load_rcc.R,
dplyr::progress_estimated().R/norm_glm.R,
dplyr::progress_estimated().tests,
DESCRIPTION,
R/normalise.R,
normalise() without removing outliers (#26).R/GSE74821.R,
data-raw root directory.R/-,
Rd files for internal functions.R/load_rcc.R and R/normalise.R.file.path() in examples and vignette.R/autoplot.R, reduce alpha for ellipses.inst/app/utils.R, set default point size (also for outliers) to 1.R/load_rcc.R, use inherits() instead of class().R/conflicts.R,
NACHO.nacho_conflicts() can be used to print conflicts.inst/app/, (#4, #5 & #14)
visualise(), to load "nacho" object from load_rcc() (previous summarise()) or from normalise().deploy() (R/deploy.R) function to easily deploy (copy) the shiny app.inst/extdata/.NACHO-analysis, which describe how to use limma or other model after using –NACHO–.DESCRIPTION,
summarise() and summarize() have been deprecated and replaced with load_rcc(). (#12 & #15)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/).R/visualise.R, R/render.R, print(), R/load_rcc.R and R/normalise.R,
check_outliers().R/visualise.R, replace datatable (render and output) with classical table. (#13)R/autoplot.R,
show_outliers to show outliers differently on plots (-i.e.-, in red).outliers_factor to highligth outliers with different point size.outliers_labels to print labels on top of outliers._S-) to remove duplicated QC metrics.R/print.R, now print a table with outliers if any (with echo = TRUE).R/GSE74821.R, dataset is up to date according to NACHO functions.DESCRIPTION, add "SystemRequirements: pandoc (>= 1.12.3) - http://pandoc.org, pandoc-citeproc".R/render.R,
opts_chunk::knitr in roxygen documentation.sessioninfo::session_info in roxygen documentation.tests/testthat/test-render.R, now checks if pandoc is available.tests/testthat/test-summarise.R, fix tests when connection to GEO is alternatively up/down between two tests.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.R/read_rcc.R, R/summarise.R,
tidyr 1.0.0 (#9).R/summarise.R,
autoplot().tidyr 1.0.0 (#9).R/normalise.R,
autoplot().outliers_thresholds component in returned object.R/visualise.R,
app object in non-interactive session.vignettes/NACHO.Rmd,
autoplot(), print() and render() (#7).results = "asis").normalise() call with custom housekeeping genes (-i.e.-, set housekeeping_predict = FALSE) (#10).tests/testthat/test-summarise.R, add condition to handle when GEOQuery is down and cannot retrieve online data.vignettes/NACHO.Rmd, add condition to handle when GEOQuery is down and cannot retrieve online data.R/summarise.R, put example in if (interactive()) {...} instead of \dontrun{...}.R/normalise.R, put example in if (interactive()) {...} instead of \dontrun{...}.R/visualise.R, put example in if (interactive()) {...} instead of \dontrun{...}.DESCRIPTION and README, description updated for CRAN, by adding “messenger-RNA/micro-RNA”.R/normalise.R, add short running example for normalise().R/visualise.R, add short running example for visualise().DESCRIPTION, description updated for CRAN, by removing some capital letters and put –NACHO– between single quotes.DESCRIPTION, title and description updated for CRAN.DESCRIPTION and vignetteDESCRIPTION, title and description updated for CRAN.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.summarise(), ssheet_csv can take a data.frame or a csv file.normalise() (and internal functions).visualise() replaces the Shiny app.summarise() and normalise() (and all internal functions).