To reference or cite the objects present in the Software Heritage archive, permalinks based on SoftWare Heritage persistent IDentifiers (SWHIDs) must be used instead of copying and pasting the url from the address bar of the browser (as there is no guarantee the current URI scheme will remain the same over time).
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bump x.y.z version to even y prior to creation of RELEASE_3_11 branch
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