CHANGES IN VERSION 1.7.10
-------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Help pages now document advanced arguments.
CHANGES IN VERSION 1.7.2
------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Dropped defunct functions.
CHANGES IN VERSION 1.5.48
-------------------------
BUG FIXES
o 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
o 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
o 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
o 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
o 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
o Added a 'digits' argument to control how to round some numerical variables
in all type of reports.
o Added a 'theme' argument to allow setting the ggplot2 theme for the plots.
BUG FIXES
o 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
o 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
o 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
o 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
o Added a vignette with an example report from bumphunter results.
CHANGES IN VERSION 1.3.5
------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Merged pull request https://github.com/leekgroup/regionReport/pull/7
o Added "template" argument to renderReport and derfinderReport to
customize the knitr template used
o 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
o 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
o Now uses derfinderPlot::vennRegions() to show venn diagram of genomic
states. Requires derfinderPlot version 1.3.2 or greater.
o 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
o 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
o 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
o 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.
o 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
o Adapted to work with bumphunter >= 1.7.6
CHANGES IN VERSION 1.1.7
------------------------
NEW FEATURES
o Users can now control 'output_format' and 'clean' options from
rmarkdown::render() when running derfinderReport()
CHANGES IN VERSION 1.1.3
------------------------
BUG FIXES
o Adapted derfinderReport() to derfinder 1.1.5
CHANGES IN VERSION 0.99.0
-------------------------
NEW FEATURES
o Preparing to submit to Bioconductor.
SIGNIFICANT USER-VISIBLE CHANGES
o Updated the vignette and the package to work with recent versions of
the packages this package depends on.
o Renamed the package from derfinderReport to regionReport and
generateReport() to derfinderReport(). In the future we will add
another report for a general GRanges object.
o Simplified derfinderReport()'s call by using advanced arguments.
o Added Travis integration.
CHANGES IN VERSION 0.0.18
-------------------------
o 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
o 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
o MA-style plots now use the scaling factor.
o 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
o Added a vignette
CHANGES IN VERSION 0.0.12
-------------------------
BUG FIXES
o complying with BiocCheck version 1.0.0
CHANGES IN VERSION 0.0.11
-------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o genomicState data moved to derfinder 0.0.53
CHANGES IN VERSION 0.0.8
------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Now requires knitrBootstrap 1.0.0
o Matches derfinder version 0.0.49
CHANGES IN VERSION 0.0.3
------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Matches derfinder version 0.0.34
CHANGES IN VERSION 0.0.1
-----------------------
NEW FEATURES
o Migrated from derfinder