Changes in version 1.23.2
SIGNIFICANT USER-VISIBLE CHANGES
- No longer suggest DESeq since this package has been deprecated.
Changes in version 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
Changes in version 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.
Changes in version 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.
Changes in version 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.
Changes in version 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.
Changes in version 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.
Changes in version 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.
Changes in version 1.21.2
SIGNIFICANT USER-VISIBLE CHANGES
- Now use GenomeIndoDb::getChromInfoFromUCSC() instead of
data(hg19Ideogram, package = 'biovizBase') to get the hg19
chromosome lengths.
Changes in version 1.19.2
SIGNIFICANT USER-VISIBLE CHANGES
- Added a NEWS.md file to track changes to the package.
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.
Changes in version 1.17.2
NEW FEATURES
- Add ORCID's following changes at
http://bioconductor.org/developers/package-guidelines/#description
Changes in version 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/
Changes in version 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
Changes in version 1.15.2
SIGNIFICANT USER-VISIBLE CHANGES
- Use BiocManager
Changes in version 1.15.1
BUG FIXES
- Fix namespace issue in relation to BiocStyle::html_document2
Changes in version 1.11.6
SIGNIFICANT USER-VISIBLE CHANGES
- Changed the default style to BiocStyle::html_document to mirror
recent changes in BiocStyle.
Changes in version 1.11.4
SIGNIFICANT USER-VISIBLE CHANGES
- Vignette now uses the new BiocStyle::html_document that was recently
released.
Changes in version 1.11.2
BUG FIXES
- Fixed the citations.
- Fixed DESeq2Report() for limma-results so that it will properly cite
limma.
Changes in version 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 case rlog() fails initially.
Changes in version 1.9.1
SIGNIFICANT USER-VISIBLE CHANGES
- Changed the default style to BiocStyle::html_document2.
Changes in version 1.7.10
SIGNIFICANT USER-VISIBLE CHANGES
- Help pages now document advanced arguments.
Changes in version 1.7.2
SIGNIFICANT USER-VISIBLE CHANGES
- Dropped defunct functions.
Changes in version 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.
Changes in version 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!
Changes in version 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.
Changes in version 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.
Changes in version 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.
Changes in version 1.5.6
SIGNIFICANT USER-VISIBLE CHANGES
- Switched to using rmarkdown instead of knitrBootstrap as the default
engine for creating the reports.
Changes in version 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).
Changes in version 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
Changes in version 1.3.6
NEW FEATURES
- Added a vignette with an example report from bumphunter results.
Changes in version 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())
Changes in version 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.
Changes in version 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).
Changes in version 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.
Changes in version 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.
Changes in version 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.
Changes in version 1.1.8
SIGNIFICANT USER-VISIBLE CHANGES
- Adapted to work with bumphunter >= 1.7.6
Changes in version 1.1.7
NEW FEATURES
- Users can now control output_format and clean options from
rmarkdown::render() when running derfinderReport()
Changes in version 1.1.3
BUG FIXES
- Adapted derfinderReport() to derfinder 1.1.5
Changes in version 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.
Changes in version 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.
Changes in version 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.
Changes in version 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.
Changes in version 0.0.13
SIGNIFICANT USER-VISIBLE CHANGES
- Added a vignette
Changes in version 0.0.12
BUG FIXES
- complying with BiocCheck version 1.0.0
Changes in version 0.0.11
SIGNIFICANT USER-VISIBLE CHANGES
- genomicState data moved to derfinder 0.0.53
Changes in version 0.0.8
SIGNIFICANT USER-VISIBLE CHANGES
- Now requires knitrBootstrap 1.0.0
- Matches derfinder version 0.0.49
Changes in version 0.0.3
SIGNIFICANT USER-VISIBLE CHANGES
- Matches derfinder version 0.0.34
Changes in version 0.0.1
NEW FEATURES
- Migrated from derfinder