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Merge branch 'master' of git.bioconductor.org:packages/phantasus
CHANGES IN VERSION 1.7.6 * Fix bug after change to stringAsFactors=FALSE CHANGES IN VERSION 1.7.4 * Removed Matrix.utils dependency CHANGES IN VERSION 1.7.3 * Volcano plot tool CHANGES IN VERSION 1.7.2 * Better GEO loader * DESeq2 experimental support * Initial support for hierarchical preloaded folder CHANGES IN VERSION 1.5.1 * Fixed hanging on empty annotation file CHANGES IN VERSION 1.3.5 * FGSEA tool * Cache + static files optimizations * Dataset permanent link feature CHANGES IN VERSION 1.3.4 * Switch to fgseaMultilevel CHANGES IN VERSION 1.3.3 * Custom order for annotation * Revamped Charts tool * AnnotationDB optimization CHANGES IN VERSION 1.3.2 * PCA plot, GSEA plot and Chart tool can be exported to SVG * Group by in column context menu * Dataset open history * Annotate dataset by AnnotateDB * Switch column datatype in context menu * GSEA plot uses general palette to color heatmap\annotation * Minor bug fixes CHANGES IN VERSION 1.1.6 * Minor bug fixes CHANGES IN VERSION 1.1.5 * PCA plot uses annotation color scheme * Rename annotation column implemented * log2(1 + x) adjust tool added * Calculated annotation revamped * Annotate dataset revamped and moved to file * Session syncing improved. * Sweep adjustment implemented CHANGES IN VERSION 1.1.3 * Option to get vertical GSEA plot * Showing heatmap along the GSEA plot * Changed filter scheme * Better session synching between fronend and backend CHANGES IN VERSION 1.1.2 * Moved to protobuf 3.4 in docker (supports messages up to 2GB) * Set exact match to be default * Set row profile as the default chart CHANGES IN VERSION 1.1.1 * Fixes in PCA plot * GSEA plotCHANGES IN VERSION 0.99.34 * Detecting conditions and replicates in GEO data CHANGES IN VERSION 0.99.28 * Submit to Enrichr tool * Changing shapes in PCA plot * Better support for OS X and Windows CHANGES IN VERSION 0.99.24 * Shiny GAM tool added * PCA plot: pretty labels, auto-redraw * Bug fixes CHANGES IN VERSION 0.99.23 * Added options "Maximum Mean Probe" and "Maximum Median Probe" to Collapse Tool * Fixed a bug emerging when one applies R-based function after collapsing by columns CHANGES IN VERSION 0.99.22 * Fixed AdjustTool * Removed obsolete output produced by servePhantasus * Updated tutorial CHANGES IN VERSION 0.99.21 * Merged changes from morpheus.js repository * Added function `reparseCachedESs` for updating downloaded GEO-datasets, which are saved in cache CHANGES IN VERSION 0.99.20 * A bit better code coverage with tests CHANGES IN VERSION 0.99.19 * Safer procedure for phenoData parsing * Even sample-empty datasets deserve to have displayed meta CHANGES IN VERSION 0.99.18 * New phenoData parsing strategy for GEO Series CHANGES IN VERSION 0.99.17 * Fixed issue with null featureData for GSE37270 CHANGES IN VERSION 0.99.16 * Fixed issue with incorrect perfomance of LimmaTool when columns are passed as args CHANGES IN VERSION 0.99.15 * Updated tutorial CHANGES IN VERSION 0.99.14 * Correct error messages when dataset is not present in GEO CHANGES IN VERSTION 0.99.13 * Added possibility to load datasets from preloaded rda-files in specialized directory on server * servePhantasus now opens browser with web-application automatically on start-up * Added tutorial on main site * Updated biocViews * Updated tutorial and mans according to changes * Added experimental support for loading RNA-seq dataset from GEO CHANGES IN VERSION 0.99.12 * Added possibility to load GEO-dataset by specifying its id in link parameters