NEWS.md

In leekgroup/regionReport: Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results

regionReport 1.23.2

SIGNIFICANT USER-VISIBLE CHANGES

• No longer suggest DESeq since this package has been deprecated.

regionReport 1.21.11

BUG FIXES

• Cropping images through 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

regionReport 1.21.10

BUG FIXES

• Add 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.

regionReport 1.21.9

BUG FIXES

• Ran another test in preparation for https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016645.html after the test in version 1.21.8 failed. The code will now be run in the example of derfinderReport() instead of the vignette.

regionReport 1.21.8

BUG FIXES

• In an attempt to fix the bug I reported at https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016645.html and in preparation to reply to this thread, I'm experimenting with suggesting that magick is installed, at which point BiocStyle will try to crop. Another option might be to use crop = NULL on all Rmd files.

regionReport 1.21.5

BUG FIXES

• The example in 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.

regionReport 1.21.4

SIGNIFICANT USER-VISIBLE CHANGES

• Add links to the example reports created when deploying the documentation website with pkgdown::deploy_to_branch(). This eliminates the need for the vignetttes/Makefile and the fake vignettes. It should also avoid confusing pkgdown.

regionReport 1.21.3

SIGNIFICANT USER-VISIBLE CHANGES

• Documentation website is now available at http://leekgroup.github.io/derfinderPlot/. It gets updated with every commit on the master branch (bioc-devel) using GitHub Actions and pkgdown.

regionReport 1.21.2

SIGNIFICANT USER-VISIBLE CHANGES

• Now use GenomeIndoDb::getChromInfoFromUCSC() instead of data(hg19Ideogram, package = 'biovizBase') to get the hg19 chromosome lengths.

regionReport 1.19.2

SIGNIFICANT USER-VISIBLE CHANGES

• Added a NEWS.md file to track changes to the package.

regionReport 1.19.2

SIGNIFICANT USER-VISIBLE CHANGES

• Renamed 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.

regionReport 1.17.2

NEW FEATURES

• Add ORCID's following changes at http://bioconductor.org/developers/package-guidelines/#description

regionReport 1.15.4

BUG FIXES

• Fix a bug in the order that was reported and fixed by @bounlu at https://github.com/leekgroup/regionReport/pull/9/

regionReport 1.15.3

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

regionReport 1.15.2

SIGNIFICANT USER-VISIBLE CHANGES

• Use BiocManager

regionReport 1.15.1

BUG FIXES

• Fix namespace issue in relation to BiocStyle::html_document2

regionReport 1.11.6

SIGNIFICANT USER-VISIBLE CHANGES

• Changed the default style to BiocStyle::html_document to mirror recent changes in BiocStyle.

regionReport 1.11.4

SIGNIFICANT USER-VISIBLE CHANGES

• Vignette now uses the new BiocStyle::html_document that was recently released.

regionReport 1.11.2

BUG FIXES

• Fixed the citations.
• Fixed DESeq2Report() for limma-results so that it will properly cite limma.

regionReport 1.11.1

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

• Made the DESeq2Report() more robust in caserlog() fails initially.

regionReport 1.9.1

SIGNIFICANT USER-VISIBLE CHANGES

• Changed the default style to BiocStyle::html_document2.

regionReport 1.7.10

SIGNIFICANT USER-VISIBLE CHANGES

• Help pages now document advanced arguments.

regionReport 1.7.2

SIGNIFICANT USER-VISIBLE CHANGES

• Dropped defunct functions.

regionReport 1.5.48

BUG FIXES

• Fixed a bug in derfinderReport() for a case when there are significant regions but not all regions have finite areas.

regionReport 1.5.43

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!

regionReport 1.5.33

NEW FEATURES

• Added the function 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.

regionReport 1.5.19

NEW FEATURES

• Added the templates templatePvalueHistogram and templateHistogram to be used with renderReport() if you prefer histogram plots instead of density plots.

regionReport 1.5.12

NEW FEATURES

• Added the function 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

• Added a digits argument to control how to round some numerical variables in all type of reports.
• Added a theme argument to allow setting the ggplot2 theme for the plots.

BUG FIXES

• Improved the PDF versions of all reports by hiding code and shortening tables. Also added a warning to switch the device to pdf for PDF output since it looks better than the default png.

regionReport 1.5.6

SIGNIFICANT USER-VISIBLE CHANGES

• Switched to using rmarkdown instead of knitrBootstrap as the default engine for creating the reports.

regionReport 1.3.8

SIGNIFICANT USER-VISIBLE CHANGES

• renderReport() and derfinderReport() now show Manhattan plots for p-value variables (p-value, q-value, FWER adjusted p-value).

regionReport 1.3.7

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

regionReport 1.3.6

NEW FEATURES

• Added a vignette with an example report from bumphunter results.

regionReport 1.3.5

SIGNIFICANT USER-VISIBLE CHANGES

• Merged pull request https://github.com/leekgroup/regionReport/pull/7
• Added template argument to renderReport() and derfinderReport() to customize the knitr template used
• Wrapped code that works in a temporary directory in with_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())

regionReport 1.3.4

NEW FEATURES

• Reports now have a link to the BibTeX file used for the references. This addresses http://f1000research.com/articles/4-105/v1#reflist Karthik Ram's bullet point number 4.

regionReport 1.3.3

NEW FEATURES

• Now uses 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).

regionReport 1.3.2

SIGNIFICANT USER-VISIBLE CHANGES

• Deprecated functions with underscores in their names in favor of camelCase functions. This was done to simplify the package.

regionReport 1.3.1

BUG FIXES

• Fixed 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.

regionReport 1.1.9

NEW FEATURES

• Introduced 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.
• You can now use the 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.

regionReport 1.1.8

SIGNIFICANT USER-VISIBLE CHANGES

• Adapted to work with bumphunter >= 1.7.6

regionReport 1.1.7

NEW FEATURES

• Users can now control output_format and clean options from rmarkdown::render() when running derfinderReport()

regionReport 1.1.3

BUG FIXES

• Adapted derfinderReport() to derfinder 1.1.5

regionReport 0.99.0

NEW FEATURES

• Preparing to submit to Bioconductor.

SIGNIFICANT USER-VISIBLE CHANGES

• Updated the vignette and the package to work with recent versions of the packages this package depends on.
• Renamed the package from derfinderReport to regionReport and generateReport() to derfinderReport(). In the future we will add another report for a general GRanges object.
• Simplified derfinderReport()'s call by using advanced arguments.
• Added Travis integration.

regionReport 0.0.18

• Now derfinderReport() has a chrsStyle argument to match changes in derfinder version 0.0.60. chrsStyle is set to UCSC by default.

regionReport 0.0.17

SIGNIFICANT USER-VISIBLE CHANGES

• Made more robust for cases where there is a small number of significant DERs: need at least 3 observations by chr for the chr to be included in the density plots.

regionReport 0.0.16

SIGNIFICANT USER-VISIBLE CHANGES

• MA-style plots now use the scaling factor.
• Using a GAM smoother instead of loess for MA-style plots. Helps for cases with many regions.

regionReport 0.0.13

SIGNIFICANT USER-VISIBLE CHANGES

• Added a vignette

regionReport 0.0.12

BUG FIXES

• complying with BiocCheck version 1.0.0

regionReport 0.0.11

SIGNIFICANT USER-VISIBLE CHANGES

• genomicState data moved to derfinder 0.0.53

regionReport 0.0.8

SIGNIFICANT USER-VISIBLE CHANGES

• Now requires knitrBootstrap 1.0.0
• Matches derfinder version 0.0.49

regionReport 0.0.3

SIGNIFICANT USER-VISIBLE CHANGES

• Matches derfinder version 0.0.34

regionReport 0.0.1

NEW FEATURES

• Migrated from derfinder

leekgroup/regionReport documentation built on May 10, 2023, 11:37 p.m.