DESCRIPTION,
include_graphics(rel_path = FALSE)."PFNF" and
"HF" plots.inst/app/,
shiny::callModule()
with shiny::moduleServer().file-arrow-up and circle-info.R/,
stringsAsFactors = FALSE from
data.frame() and as.data.frame() calls, where
it is the default since R 4.0.0.outliers = FALSE
instead of outlier.shape = NA.vignettes/, README.Rmd and the
render() report template,
#| YAML comments, which
needs knitr 1.35 or newer.pak::pak()
instead of remotes::install_github().vignettes/,
NS_H_miR_1.4 CodeSet, since its two CodeSets come from
different nSolver versions and load_rcc() refuses files
that mix versions.dcast() and as.data.table().pkgdown/,
R/normalise.R, R/load_rcc.R and
vignettes/NACHO.Rmd,
raw_counts and
normalised_counts slots, which never existed, and say that
nacho holds one row per sample and probe.R/GSE74821.R,
GSE74821 holds 48 samples, not 20.inst/CITATION,
person() objects, so the
citation shows their full initials and spells Leen M. ’t Hart
correctly.R/autoplot.R,
colour for the control probe
plots."PFNF" and
"HF" plots to the panel edges without log-10 warnings about
infinite values."BD",
"FoV", "PCL", "LoD",
"PN", "Positive", "Negative" and
"Housekeeping" plots, which drew every point at one
position and dropped some of them.R/render.R,
outliers_labels = "CartridgeID" works and column names with
quotes no longer break the report.inst/app/app.R,
all.rdata debug file to the
working directory when uploading RCC files.suppressMessages() received x instead of
expr.ssheet_dt.DESCRIPTION,
visualise() ask for it when it is not installed.
The deploy() help page notes that the server needs it
too.R/geometric_housekeeping.R,
House_factor. (#53)R/qc_pca.R,
PC01 to PC10 and the variance
explained change, and the PCA plots now show the main sources of
variation between samples.R/normalise_counts.R,
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.R/qc_pca.R and R/normalise_counts.R,
load_rcc() again to refresh them.R/normalise.R,
n_comp passed to normalise(),
which was ignored.is_outlier when only the thresholds
change.R/qc_features.R, R/qc_limit_detection.R
and R/check_outliers.R,
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.R/load_rcc.R,
plexset_id S1 to S8 when the
sample sheet lists each file once.data.table.R/print.R,
print().data/,
GSE74821 with the corrected PCA and
normalised counts.inst/app/,
application/zip, and
.RCC, .rcc, .RCC.gz and
.csv files in any case.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 highlight 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 R Markdown
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).