NEWS

---

phantasus 1.23.4

• read.gct/write.gct functions are moved to phantasusLite package

phantasus 1.23.3

• Changed a configuration scheme
• setupPhantasus() now can be used to generate a config
• Support for remote count files via HSDS

phantasus 1.21.3

• Advanced normalizations: TMM & voom
• Complex differential expression design for limma & DESeq2
• Rework of count meta files (breaks backward compatibility)

phantasus 1.19.3

• Shiny GAM -> Shiny GATOM

phantasus 1.17.5

• All GEO datasets with <100K rows can be loaded

phantasus 1.17.4

• Updated DESeq2 usage

phantasus 1.15.7

• Using relative paths in counts metadata

phantasus 1.15.5

• Fix windows-related bug in tests

phantasus 1.15.3

• Major rework of RNA-seq counts support from external hdf5 files (like ARCHS4)
• Fix typing bug

phantasus 1.15.1

• Option to omit gene version IDs (like in ENSEMBL) before conversion
• Annotations are trasnmitted with type information, which fixes many bugs

phantasus 1.9.5

• Support for preloaded sessions

phantasus 1.9.3

• Changed Dockerfile to nginx+rApache (default ports are changed)

phantasus 1.7.6

• Fix bug after change to stringAsFactors=FALSE

phantasus 1.7.4

• Removed Matrix.utils dependency

phantasus 1.7.3

• Volcano plot tool

phantasus 1.7.2

• Better GEO loader
• DESeq2 experimental support
• Initial support for hierarchical preloaded folder

phantasus 1.5.1

• Fixed hanging on empty annotation file

phantasus 1.3.5

• FGSEA tool
• Cache + static files optimizations
• Dataset permanent link feature

phantasus 1.3.4

• Switch to fgseaMultilevel

phantasus 1.3.3

• Custom order for annotation
• Revamped Charts tool
• AnnotationDB optimization

phantasus 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

phantasus 1.1.6

• Minor bug fixes

phantasus 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

phantasus 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

phantasus 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

phantasus 1.1.1

• Fixes in PCA plot
• GSEA plotCHANGES IN VERSION 0.99.34
• Detecting conditions and replicates in GEO data

phantasus 0.99.28

• Submit to Enrichr tool
• Changing shapes in PCA plot
• Better support for OS X and Windows

phantasus 0.99.24

• Shiny GAM tool added
• PCA plot: pretty labels, auto-redraw
• Bug fixes

phantasus 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

phantasus 0.99.22

• Fixed AdjustTool
• Removed obsolete output produced by servePhantasus
• Updated tutorial

phantasus 0.99.21

• Merged changes from morpheus.js repository
• Added function 'reparseCachedESs' for updating downloaded GEO-datasets, which are saved in cache

phantasus 0.99.20

• A bit better code coverage with tests

phantasus 0.99.19

• Safer procedure for phenoData parsing
• Even sample-empty datasets deserve to have displayed meta

phantasus 0.99.18

• New phenoData parsing strategy for GEO Series

phantasus 0.99.17

• Fixed issue with null featureData for GSE37270

phantasus 0.99.16

• Fixed issue with incorrect perfomance of LimmaTool when columns are passed as args

phantasus 0.99.15

• Updated tutorial

phantasus 0.99.14

• Correct error messages when dataset is not present in GEO

phantasus 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

phantasus 0.99.12

• Added possibility to load GEO-dataset by specifying its id in link parameters