NEWS

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ReportingTools 2.7.1

• Updated email for Jessica L. Larson

ReportingTools 2.3.8

• Minor bug fixes in NAMESPACE and DESCRIPTION and css
• Enhanced vignettes to include information on our website and publication
• Enhanced vignettes to clarify use of .modifyDF()

ReportingTools 2.0.0

• HTML reports are now represented by the HTMLReportRef referenceClass
• HTML output now fully customizable via .toHTML, .toDF and .modifyDF arguments to publish (see vignette)
• Publication mechanism is abstracted and customizable via ReportHandlers class
• ReportingTools output can be used within knitr documents and shiny Web applications (see vignettes knitr.Rmd and shiny.Rnw)
• Persistent representation of the HTML report being created is stored and accessible in the .reportDOM field of HTMLReportRef objects
• [[ and [[<- methods created for HTMLReportRef objects which allow selection, replacement and insertion of objects directly into reports
• Publish generic now accepts a 'name' argument.
• Existing reports can be read in via readReport, modified (via publish, [[<-, or direct manipulation of .reportDOM), and rewritten to file
• Path generic now returns a list/vector of the location slot values of the attached ReportHandlers object(s). These can be paths, connections, or other indications of report destination.
• Link generic function provided to build tables/sets of HTML links
• Added support for publishing ggbio and recordedplot objects
• CSS changed to Twitter Bootstrap
• Bugfixes to how NAs are handled when filtering and sorting columns
• New methods to handle output from running a glmLRT test in edgeR or nbinomTest in DESeq
• DEPRECATED: HTMLReport class is superseded by HTMLReportRef
• DEPRECATED: publication of HTMLReportRefs directly to a report (in order to make an index page) is no longer supported. Use the Link function.
• DEPRECATED: the page generic is not meaningful for HTMLReportRef objects (not all of which have a corresponding connection) and is deprecated. Use path instead.