NEWS.md
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.html
BUG 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
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 caserlog() fails initially.SIGNIFICANT USER-VISIBLE CHANGES
BiocStyle::html_document2.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/v1
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.NEW FEATURES
output_format and clean options from rmarkdown::render() when running derfinderReport()
NEW 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