SIGNIFICANT USER-VISIBLE CHANGES
DESeq since this package has been deprecated.BUG FIXES
magick::image_trim() as done by default by
BiocStyle::html_document() can fail on Linux. This could be an ImageMagick
issue or an issue about lack of resources. The full investigative report is at
https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016650.html.
This is related to:
https://github.com/yihui/knitr/issues/1785#issuecomment-574723631
https://github.com/yihui/knitr/issues/1796
https://github.com/Bioconductor/BiocStyle/issues/65#issuecomment-552832630
https://github.com/ropensci/magick/issues/171
https://github.com/ropensci/magick/issues/194
In regionReport version 1.21.10 I have opted by using crop = NULL to disable
cropping of images by BiocStyle::html_document() and thus avoid the
issues with ImageMagick either coming from magick, from the version of
ImageMagick installed on the Linux Bioconductor build machine and devel
docker, or from resources in these two Linux environments as described in the
investigative report.
About a month ago I also saw failures on Windows on Bioc 3.10. Whether they were
caused by ggbio 1.35.1 or this issue will remain a mystery. But it's likely
that this magick::image_trim() issue also affected the Bioconductor windows
builder.
The related bioc-devel threads are:
https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016538.html
https://stat.ethz.ch/pipermail/bioc-devel/2020-March/016365.htmlBUG FIXES
crop = NULL to all template Rmarkdown files. Drop magick as a
depencency since cropping is not used on the reports (as done through
BiocStyle by default). This is again related to responding to
https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016645.html.BUG FIXES
derfinderReport() instead of the vignette.BUG FIXES
magick is installed, at which point BiocStyle will try to crop. Another
option might be to use crop = NULL on all Rmd files.BUG FIXES
renderReport() was failing because the first time the
function was called, it ran derfinder::makeGenomicState() which in turn
uses GenomicFeatures::isActiveSeq(). derfinder version 1.21.5 fixed this
bug and is thus required by regionReport now.SIGNIFICANT USER-VISIBLE CHANGES
pkgdown::deploy_to_branch(). This eliminates the need for
the vignetttes/Makefile and the fake vignettes. It should also avoid
confusing pkgdown.SIGNIFICANT USER-VISIBLE CHANGES
SIGNIFICANT USER-VISIBLE CHANGES
GenomeIndoDb::getChromInfoFromUCSC() instead of
data(hg19Ideogram, package = 'biovizBase') to get the hg19 chromosome lengths.SIGNIFICANT USER-VISIBLE CHANGES
NEWS.md file to track changes to the package.SIGNIFICANT USER-VISIBLE CHANGES
load_install() as load_check() as this function now only checks
that the package(s) was installed and returns an error if missing. The
error shows the user how to install the package(s) they are missing
instead of installing them automatically. This complies with Marcel
Ramos' request at https://github.com/leekgroup/recount/issues/14.NEW FEATURES
BUG FIXES
BUG FIXES
Fixed an issue with DESeq2Exploration.Rmd that affected both
DESeq2Report() and edgeReport(). This should also fix the recount
bioc-release (3.7) and bioc-devel (3.8) branches.
Fixed a NAMESPACE issue with rmarkdown::html_document and
BiocStyle::html_document
SIGNIFICANT USER-VISIBLE CHANGES
BUG FIXES
BiocStyle::html_document2SIGNIFICANT USER-VISIBLE CHANGES
BiocStyle::html_document to mirror recent
changes in BiocStyle.SIGNIFICANT USER-VISIBLE CHANGES
BiocStyle::html_document that was recently
released.BUG FIXES
DESeq2Report() for limma-results so that it will properly cite
limma.SIGNIFICANT USER-VISIBLE CHANGES
DESeq2Report() can now be used with other software if their results are
made to look like DESeq2 results. For example, with limma-voom results.BUG FIXES
DESeq2Report() more robust in case rlog() fails initially.SIGNIFICANT USER-VISIBLE CHANGES
BiocStyle::html_document2.SIGNIFICANT USER-VISIBLE CHANGES
SIGNIFICANT USER-VISIBLE CHANGES
BUG FIXES
derfinderReport() for a case when there are significant
regions but not all regions have finite areas.SIGNIFICANT USER-VISIBLE CHANGES
edgeReport() now includes two edgeR specific plots: one showing the BCV
and another showing a 2-dim MDS. Also added more edgeR citations that I
missed earlier: thank you Gordon Smyth!NEW FEATURES
edgeReport() for creating HTML or PDF reports based on
edgeR results. Together with DESeq2Report() now regionReport supports
the two most used packages for RNA-seq feature-level analysis.NEW FEATURES
templatePvalueHistogram and templateHistogram
to be used with renderReport() if you prefer histogram plots instead
of density plots.NEW FEATURES
DESeq2Report() for creating HTML or PDF reports based
on DESeq2 results. This should also be useful to explore derfinder
results created from the expressed regions-level approach.SIGNIFICANT USER-VISIBLE CHANGES
digits argument to control how to round some numerical variables
in all type of reports.theme argument to allow setting the ggplot2 theme for the plots.BUG FIXES
pdf for PDF
output since it looks better than the default png.SIGNIFICANT USER-VISIBLE CHANGES
rmarkdown instead of knitrBootstrap as the default
engine for creating the reports.SIGNIFICANT USER-VISIBLE CHANGES
renderReport() and derfinderReport() now show Manhattan plots for p-value
variables (p-value, q-value, FWER adjusted p-value).NEW FEATURES
renderReport() now has the densityTemplates argument via which users can
customize the density plots for the p-value variables and the continuous
variables. This addresses one of David Robinson's requests at
http://f1000research.com/articles/4-105/v1NEW FEATURES
SIGNIFICANT USER-VISIBLE CHANGES
template argument to renderReport() and derfinderReport() to
customize the knitr template usedwith_wd() function,
which evaluates in the directory but returns to the original directory
in the case of a user interrupt or error (with on.exit())NEW FEATURES
NEW FEATURES
derfinderPlot::vennRegions() to show venn diagram of genomic
states. Requires derfinderPlot version 1.3.2 or greater.derfinderReport() now has a significantVar argument that allows users to
choose between determining significant regions by P-values, FDR adjusted
P-values, or FWER adjusted P-values (if FWER adjusted P-values are
absent, then FDR adjusted P-values are used instead, with a warning).SIGNIFICANT USER-VISIBLE CHANGES
BUG FIXES
renderReport() and derfinderReport() so they'll open the correct URL
when interactive() == TRUE and the user has knitrBootstrap version 0.9.0
installed instead of the latest GitHub version.NEW FEATURES
renderReport() which creates a simple exploratory report for
any set of genomic regions. It allows the user to further customize the
report by using a child file.output_format advanced parameter on both
renderReport() and derfinderReport() to output a PDF file instead
of an HTML file. The interactive tables are lost and only the top 20
rows are shown.SIGNIFICANT USER-VISIBLE CHANGES
bumphunter >= 1.7.6NEW FEATURES
output_format and clean options from
rmarkdown::render() when running derfinderReport()BUG FIXES
derfinderReport() to derfinder 1.1.5NEW FEATURES
SIGNIFICANT USER-VISIBLE CHANGES
derfinderReport to regionReport and
generateReport() to derfinderReport(). In the future we will add
another report for a general GRanges object.derfinderReport()'s call by using advanced arguments.derfinderReport() has a chrsStyle argument to match changes in
derfinder version 0.0.60. chrsStyle is set to UCSC by default.SIGNIFICANT USER-VISIBLE CHANGES
SIGNIFICANT USER-VISIBLE CHANGES
SIGNIFICANT USER-VISIBLE CHANGES
BUG FIXES
BiocCheck version 1.0.0SIGNIFICANT USER-VISIBLE CHANGES
genomicState data moved to derfinder 0.0.53SIGNIFICANT USER-VISIBLE CHANGES
knitrBootstrap 1.0.0derfinder version 0.0.49SIGNIFICANT USER-VISIBLE CHANGES
derfinder version 0.0.34NEW FEATURES
derfinder