https://github.com/ctlab/phantasus
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Tip revision: fe9c3824eb3d9649de2d0c074c8896ae13c45f27 authored by Nitesh Turaga on 27 April 2020, 19:14 UTC
bump x.y.z version to even y prior to creation of RELEASE_3_11 branch
Tip revision: fe9c382
NEWS
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

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