Changes in version 1.1.6 ---------------------------------------------------------------- CODE * Changes in summaryIntervals in order to allow the exploration at pool levels, useful when a targeted sequencing involving several PCR pools was performed. * plotAttrPerform method was added. This function produces a ggplot graph illustrating relative and cumulative frequencies of features in attribute intervals. If the panel has several pools, then the graph shows the mentioned results for each pool. Changes in version 1.1.2 ---------------------------------------------------------------- CODE * Changes in buildFeaturePanel in order to reduce the run time. Now, the pileupCounts is not called, thus the pileup matrix is not built. Instead it, coverage and others Rsamtools and IRanges methods are used. * readPercentages and plotInOutFeatures methods were added in order to explore experiment efficiency. * biasExploration and plotMetaDataExpl were added in order to perform bias sources exploration. The first allows the gc content, feature length or other source distribution exploration. The second implement a plot in which attribute distribution for each source bias quartile or group is explored. VIGNETTE * English correction and new methods incorporation Changes in version 1.1.1 ---------------------------------------------------------------- CODE * In setters and initialize functions, examples were updated to shorten elapsed times (only interactive). Thanks to V. Obenchain VIGNETTE * Elapsed times reduction using TarSeqQC data example instead of building myPanel from scratch. Thanks to V. Obenchain Changes in version 1.1.0 ---------------------------------------------------------------- DOCUMENTATION * Bumped version number of all packages after creation of 3.2 branch Changes in version 1.0.0 ---------------------------------------------------------------- DOCUMENTATION * First release Changes in version 0.99.9 ---------------------------------------------------------------- CODE * Modifications in pileupCounts in order to consider stranded counts * Changes in plot methods. arrangeGrob from gridExtra was changed by plot_grid form cowplot package. * Update the package vignette. Changes in version 0.99.8 ---------------------------------------------------------------- CODE * Modifications in pileupCounts and buildFeaturePanel in order to process overlapped features. * Wrap plotting examples. Changes in version 0.99.7 ---------------------------------------------------------------- CODE * Modifications in pileupCounts and buildFeaturePanel in order to process overlapped features. * Modifications in bedFile building in order to remove duplicated features based on duplicated start, end and chromosome definitions. Changes in version 0.99.6 ---------------------------------------------------------------- CODE * Definition of pileupCounts as a function instead a TargetExperiment S4 method. * Adaptation and optimization of pileupCounts and bplapply usage in the buildFeaturePanel method. Changes in version 0.99.4 ---------------------------------------------------------------- DESCRIPTION file * Modification of the Rsatmools version dependency. Changes in version 0.99.3 ---------------------------------------------------------------- CODE * Modifications in buildFeaturePanel and summarizePanel for a correct implementation of parallel computing. Changes in version 0.99.2 ---------------------------------------------------------------- CODE * BiocParallel was used instead of parallel package for parallel computing. Changes in version 0.99.1 ---------------------------------------------------------------- DOCUMENTATION * The example data has been compiled using Bioconductor 3.2 packages. Changes in version 0.99.0 ---------------------------------------------------------------- DOCUMENTATION * `NEWS` file was added.