NEWS/CHANGELOG R4RNA_1.0.0 2015-10-27 (Daniel Lai ) - Now accepts Biostrings XStringSet as valid multiple sequence alignment input - Removed readFasta and writeFasta functions, please use readBStringSet and writeXStringSet instead. - colourByValue handles single value and empty helix cases - isConflictingHelix, isDuplicatingHelix and isOverlapping helix now return a decimal value from 0 to 1 instead of a FALSE or TRUE value when faced classifying a single helix with multiple basepairs. This leaves the thresholding up to the user and the functions are also A LOT faster. - added asp option to plots R4RNA_0.1.4.tar.gz 2012-03-21 (Daniel Lai ) - Addition of structureMismatchScore and sequencePercentGaps - Added "pad" parameter for specifying padding in blankPlot - Added "no.par" option to blankPlot, to allow for par(mfrow = ...), etc - Replaced conflict.filter for conflict.col and conflict.lty in plotCovariance - Fixed bug in collapseHelix R4RNA_0.1.3.tar.gz 2012-02-16 (Daniel Lai ) - Updated vignette, obtained via vignette("R4RNA") R4RNA_0.1.2.tar.gz 2012-02-15 (Daniel Lai ) - Improved colourBy functions (default arguments + get option) - Addition of basepairFrequency and colourByBasepairFrequency - Addition of log space operations, logseq, logfloor, logceiling - Updated examples in manual to reflect changes R4RNA_0.1.1.tar.gz 2012-02-14 (Daniel Lai ) - Package revised for publication in NAR Method Online - Functions streamlined for improved user experience - Addition of various "ColourBy" functions - Addition of alignment statistics functions - File reading functions made robust and able to handle multiple entries - Various format conversion functions to and from helix - Addition of plotDoubleCovariance and plotOverlapCovariance functions - Addition of a lot of fine-tuning paramters for plotCovariance - Expanded role and functionality of blankPlot - Allows for direct output as png or pdf files - Improved and expanded documentation R4RNA_0.1.0.tar.gz 2011-12-16 (Daniel Lai ) - Initial public release