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,
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,
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).