2015-3-27: version 2.7.1 ------------------------ - Updated email for Jessica L. Larson 2013-4-1: version 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() 2013-4-1: version 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methods to handle output from running a glmLRT test in edgeR or nbinomTest in DESeq - DEPRECATED: HTMLReport class is superseded by HTMLReportRef - DEPRECATED: publication of HTMLReportRefs directly to a report (in order to make an index page) is no longer supported.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.