Changes in version 1.31.1 o dedicated docker server script to reduce memory usage o fixes in annotation parsing Changes in version 1.25.5 o reworked annotation parsing Changes in version 1.23.4 o read.gct/write.gct functions are moved to phantasusLite package Changes in version 1.23.3 o Changed a configuration scheme o setupPhantasus() now can be used to generate a config o Support for remote count files via HSDS Changes in version 1.21.3 o Advanced normalizations: TMM & voom o Complex differential expression design for limma & DESeq2 o Rework of count meta files (breaks backward compatibility) Changes in version 1.19.3 o Shiny GAM -> Shiny GATOM Changes in version 1.17.5 o All GEO datasets with <100K rows can be loaded Changes in version 1.17.4 o Updated DESeq2 usage Changes in version 1.15.7 o Using relative paths in counts metadata Changes in version 1.15.5 o Fix windows-related bug in tests Changes in version 1.15.3 o Major rework of RNA-seq counts support from external hdf5 files (like ARCHS4) o Fix typing bug Changes in version 1.15.1 o Option to omit gene version IDs (like in ENSEMBL) before conversion o Annotations are trasnmitted with type information, which fixes many bugs Changes in version 1.9.5 o Support for preloaded sessions Changes in version 1.9.3 o Changed Dockerfile to nginx+rApache (default ports are changed) Changes in version 1.7.6 o Fix bug after change to stringAsFactors=FALSE Changes in version 1.7.4 o Removed Matrix.utils dependency Changes in version 1.7.3 o Volcano plot tool Changes in version 1.7.2 o Better GEO loader o DESeq2 experimental support o Initial support for hierarchical preloaded folder Changes in version 1.5.1 o Fixed hanging on empty annotation file Changes in version 1.3.5 o FGSEA tool o Cache + static files optimizations o Dataset permanent link feature Changes in version 1.3.4 o Switch to fgseaMultilevel Changes in version 1.3.3 o Custom order for annotation o Revamped Charts tool o AnnotationDB optimization Changes in version 1.3.2 o PCA plot, GSEA plot and Chart tool can be exported to SVG o Group by in column context menu o Dataset open history o Annotate dataset by AnnotateDB o Switch column datatype in context menu o GSEA plot uses general palette to color heatmap\annotation o Minor bug fixes Changes in version 1.1.6 o Minor bug fixes Changes in version 1.1.5 o PCA plot uses annotation color scheme o Rename annotation column implemented o log2(1 + x) adjust tool added o Calculated annotation revamped o Annotate dataset revamped and moved to file o Session syncing improved. o Sweep adjustment implemented Changes in version 1.1.3 o Option to get vertical GSEA plot o Showing heatmap along the GSEA plot o Changed filter scheme o Better session synching between fronend and backend Changes in version 1.1.2 o Moved to protobuf 3.4 in docker (supports messages up to 2GB) o Set exact match to be default o Set row profile as the default chart Changes in version 1.1.1 o Fixes in PCA plot o GSEA plotCHANGES IN VERSION 0.99.34 o Detecting conditions and replicates in GEO data Changes in version 0.99.28 o Submit to Enrichr tool o Changing shapes in PCA plot o Better support for OS X and Windows Changes in version 0.99.24 o Shiny GAM tool added o PCA plot: pretty labels, auto-redraw o Bug fixes Changes in version 0.99.23 o Added options "Maximum Mean Probe" and "Maximum Median Probe" to Collapse Tool o Fixed a bug emerging when one applies R-based function after collapsing by columns Changes in version 0.99.22 o Fixed AdjustTool o Removed obsolete output produced by servePhantasus o Updated tutorial Changes in version 0.99.21 o Merged changes from morpheus.js repository o Added function `reparseCachedESs` for updating downloaded GEO-datasets, which are saved in cache Changes in version 0.99.20 o A bit better code coverage with tests Changes in version 0.99.19 o Safer procedure for phenoData parsing o Even sample-empty datasets deserve to have displayed meta Changes in version 0.99.18 o New phenoData parsing strategy for GEO Series Changes in version 0.99.17 o Fixed issue with null featureData for GSE37270 Changes in version 0.99.16 o Fixed issue with incorrect perfomance of LimmaTool when columns are passed as args Changes in version 0.99.15 o Updated tutorial Changes in version 0.99.14 o Correct error messages when dataset is not present in GEO Changes in version 0.99.13 o Added possibility to load datasets from preloaded rda-files in specialized directory on server o servePhantasus now opens browser with web-application automatically on start-up o Added tutorial on main site o Updated biocViews o Updated tutorial and mans according to changes o Added experimental support for loading RNA-seq dataset from GEO Changes in version 0.99.12 o Added possibility to load GEO-dataset by specifying its id in link parameters