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CHANGELOG
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v0.1.1
* First stable version
v0.2.0
* Improvements on data proxy
* Improvements on error manager
* Improvements on network manager
* Improvements in security (ssl, https)
* General improvements
* Improve installers
* Layout improvements
* Created encryption component (images encrypted)
* Created new log in component (no authorization needed)
* Bug fixes
* New visual features (selection, composite genes, export selection and heat map)
v0.3.1
* Improved log in component
* Added new ST logo
* Added options to dataset page (edit, remove, open)
* New data model
* Major refactor of main components
* New data adquisition component
* New rendering component
* Many bug fixes
* Many speed optimizations
* New rendering options and new color modes
* Cell view now has the selections table
* Options to store and export selections
* New mechanism to show and change color of genes
* Many new graphical options in cell view
* New Analysis Page (edit, remove, export)
* First version of DDA in analysis page
v0.3.2
* (TODO)
v0.3.3
* (TODO)
v0.3.4
* Made dots default size smaller
* Force color dialog for genes to be always on top
v0.3.5
* Fixed a bug that caused the viewer to crash when
a user with deprecated old selections-datasets
entered the datasets view.
v0.3.6
* Added an option to export features in the cell view for a selection
* Fixed a bug that would case the DEA Dialog to be un-stable sometimes
* Ensure the dot size is 0.5 by default
v0.4.0
* New UI design
* Improved speed and performance
* Improve memmory loading
* New color computation options (log, exp and normal)
* New pooled modes (reads, genes and TPMs)
* Improved windows and mac installers
* Many bug fixes
* Streaming JSON parsing
* Async Network downloads
* Improved error management
* Improved error messages
v0.4.1
* Fixed a bug with the selection rubberband
* Fixed a bug with the log in dialog in windows
* Fixed a bug causing a segmentation fault when exiting
* Fixed a bug with the caching of usernames
v0.4.2
* Added a threshold for genes
* Improved rendering code
* Adjust legend so it changes numbers with gene/reads threshold
* Some improvemends in the DEA
v0.4.3
* Fixed some bugs with the thresholds
* Removed async rendering data computation
* Restored OpenGLFunctions for compatibility reasons
v0.4.4
* Replaced table in DEA to fix some bugs
* Fixed a bug in selections table in the sorting of columns
* Added search box for DEA table
* Fixed a bug in the DEA threholds
* Fixed a bug in the minimum value for genes threshold
v0.4.5
* Some updates in DEA layout
* Scatter plot in DEA now scales
* Scatter plot will highlight the selected gene in the table
* Reg Exp now allows to turn visible genes that are not
* Partially removed use of Qt3D (GeneRendereGL uses Qt OpenGL)
* Faster rendering
* Fixed bug that would cause the app to crash when turning cell tissue off
v0.4.6
* Fixed a small bug in the genes threshold
v0.4.7
* Added support to store and view a snapshot of the tissue when saving selections
* Fixed a bug in the reg-exp with the string matching
* Fixed a bug with the reg-ex not selecting all genes in feature
v0.4.8
* Added option to toggle legend values by genes or reads
* Fixed some artifacts bugs in the rendering
* Improved init-reset of graphical elements
* Changed text in reg-exp widget
* Removed dependency with Qt3D
v0.4.9
* Made some general clean up and optimization
* Fixed a bug in the computation of TPM correlation values in DEA
v0.5.0
* Replaced QOpenGLWindows for QOpenGLWidgets
* Introduced QOpenGLFunctions for compatibility
* Fix some cppcheck warnings
* Added total reads per feature threshold
* Fixed some errors in the computation of correlation in DEA
v0.5.1
* Perform total genes/reads filter for total genes/reads in each feature
regardless of how many genes are selected
* Fix a bug when doing reg-exp selection on genes that should not appear
in some features due to threshold restraints
v0.5.2
* Show total reads and total genes in selection widget
v0.5.5
* Changed UI interface
* Added option to load datasets locally
* Improved functionality in datasets view
* Improved functionality in selections view
* Selections do not get automatically saved in the cloud
* Added gene based cut-off
* Updated license terms
* Removed deprecated libraries
* General improvements and bug fixes
v0.5.6
* Fixed many bugs
* Clean up and refactored the code a bit
* Added no internet configuration trough CMake
* Added option to disable individual reads cut off
* Added option to remove multiple datasets/selections
* Users only see their datasets/selections
v0.5.7
* Fixed some bugs
* Increased speed by adding back Qt containers
* Removed VAOs and buffers in the gene renderer
v0.5.8
* Fixed small bugs
* Added an option to create selection object when the user needs
v0.6.0
* Fixed small bugs
v0.6.1
* Added network settings as a config file
* Simplified importing of datasets
v0.6.2
* Removed plotting library/functionalities
v0.6.3
* Added back plotting functionalities
* Fixed the building and packing for all the platforms
v0.7.0
* Removed the online support
* Datasets are now loaded manually in different ways
* Added support to include a file with spot coordinates in the dataset
* Added support to include a file with spike-ins in the dataset
* Added support to include a file with normalization factors in the dataset
* Added support to adjust the chip size in the dataset
* Datasets are now working with the latest matrix TSV format
* If no spot coordinates are given the alignment matrix will be computed automatically
* Added a view with the spots to allow: select, show, hide, color, etc...
* Added the total count for the Genes and Spots view
* Added right-click support for tables
* Added widget to show QC stats
* Added option to load gene colors
* Added option to load spot colors
* Added option to perform clustering on a dataset
* Added option to select based on the clustered spots
* Added lasso selection
* Added option to export/import selections
* Selections are now sub-matrices of a dataset
* Added widget to compute correlation between 2 selections
* Added widget to compute DEA (Differential Expression Analysis) between 2 selections
* Added widget to compute PCA between selections
* Added option to merge selections
* Bug fixes and improvements
* UI optimizations
* Speed improvements
* Removed deprecated stuff
v0.7.1
* Fixed bugs
* Bumped up the SCRAN code to the latest release (new API)
v0.7.5
* Removed Scran and DESeq2 normalisation from the main view
* Removed the update bottom in the visualisation settings
* Fixed a bug when viewing spots when there are no genes shown
* Added EdgeR to the methods options for the DEA widget
* Enforce Scran normalisation in the DEA widget
* Optimized the Scran normalisation settings in general
* Bumped R to 3.5
V0.8.0
* Added support for 3D datasets
* Removed R dependencies
* Removed some unuseful functionalities
* Simplified the DEA
* Simplified the normalization and filtering
* Increase in speed (multi-threading and optimizations)
* More robust and efficient
* Added cluster info to spots panel
* Enabled to select spots from spots panel
v0.8.1
* Added support for more formats for the spot coordinates file
v0.8.3
* Fixed a bug related to missing spots in MAC OS Catalina
v0.8.4
* Windows versions working
V0.8.5
* Big speed improvements
* Fixed bug when computing histograms
* Made spots smaller when they are selected
v0.8.9
* Added clusters widget to interact with clusters
* Improvements in the computation of the rendering data
* Improvements in the visualization 2D/3D
* General bug fixes and improvements