...

...

10.0.

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21.

...

• A critical bug fix on deleting a task in imported projects

9.0.20.1025

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0509

• Added a feature of allowing manually type in a list of features to color in scatterplot
• Added annotate Visium task to add tissue position and image information on 10X Genomics Visium data
• Added compute biomarker as an independent task in addition to the subtask in any classification task
• Improved the Seurat3 integration task
• Enable both Monocle 2 and Monocle 3 in trajectory analysis
• Added download options for mm39 assembly library files
• Minor bug fixes

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10.0.

...

21.

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0411

• Added number of genes for up and down regulation separately in volcano plot
•  Annotate Visium task to add tissue position and image information on 10X Genomics Visium data
• Minor bug fixes

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10.0.

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21.

...

• Improved the speed on list management page display
• Sped up the single cell fastq files process tasks
• Improved importing ENA projects
• Improved DESeq2 differential analysis
• Minor bug fixes

9.0.20.0819

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0328

• Added HTSeq quantification method to Microarray data analysis
• Added BWA method on ERCC in pre-alignment QA/QC
• Added project statistics information on homepage
• Improvement Monocle 3 (trajectory analysis) to automatically detect the input data is in log scale or not
• Minor bug fixes

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10.0.

...

21.

...

• Move Help to menu bar on the top of the homepage (from Settings)
• Added DESeq2 differential analysis task
• Upgrade distributed JRE to the most recent release version
• Minor bug fixes

9.0.20.0720

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0302

• Upgrade trajectory analysis using monocle 3 algorithm
• Added bubble map shortcut in data viewer
• Added function to specify gene list in filter feature dialog without creating a list beforehand
• Added more options in usage report
• Changed the graph-based clustering nearest neighbor type default from KNN to NN-Descent
• Improvement on interface
• Minor bug fixes

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10.0.

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21.

...

• Fixed split by attributes issue
• Fixed PCA issue

9.0.20.0622

• Fixed some aligner issues

9.0.20.0616

• Improved the speed on user interface
• Fixed the reset password issue

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0201

• Added publish cell attributes to project task
• Scatterplot selection labeling is turned off by default
• Minor bug fixes

10.0.21.0117

• Added more options to generate usage report
• Added more configuration options in BWA-MEM
• Added download to the user management table
• Minor bug fixes

10.0.20.

...

• Added file transfer function on Flow homepage
• Single cell classification result is project level single cell attribute, it can be managed on the data tab
• Improved data tab interface
• Added volcano plot as a separate plot type in data viewer
• Added functionality on configuring axis title and label in data viewer plot
• Added library file sharing preference in user preference page
• Added importer on .tsv file format
• Improved orphaned file verification
• Bug fixes

9.0.20.0526

• Improved bioproject download from ENA
• Added configuration on plot title
• Added ability to select points on scatterplot legend
• Allow trajectory analysis to be performed on PCA output node
• Bug fixes 

9.0.20.0510

• Added trajectory analysis report into data viewer
• Added color configuration on box-whisker plot and violin plot
• Added .pdf option to data viewer download file format
• Bug fixes 

9.0.20.0426

• Added importer on data files from single cell portal site
• Bug fixes 

9.0.20.0421

• Move Single cell QA/QC plot into data viewer
• Added more functionalities on user added task module
• Improved the speed on tSNE computation
• Bug fixes

9.0.20.0406

• Added ability to share library files at different levels
• Improved the user interface on data viewer
• Added importer on Seurat object
• Added split matrix data node by categorical attribute
• Separated PCA calculation from UMAP, tSNE, Graph-based clustering analysis
• Upgrade STAR aligner to 2.7.3a
• Added ability to combine multiple attributes into one
• Added ability to change the data node label
• Added task to down-sampling single cells
• Removed blank plot in data viewer
• Improved speed and memory usage on multiple tasks
• Bug fixes

9.0.20.0202

• Add a separate link to the input information in the task detailed page
• Performance improvement and bug fixes

9.0.20.0121

• Performance improvement
• Minor bug fixes

9.0.20.0110

• Improved .bcl file importer for data generated from the 10X Genomics platform
• Dot plot is integrated into the data viewer
• Volcano plot is integrated into the data viewer
• Enhanced configuration ability of axes ranges in data viewer plots
• Added support for cell annotation files in .csv format
• Changed UMAP initialize output values default settings to random from spectral
• Minor bug fixes

9.0.19.1222

• Improvement on the performance of data viewer
• Improvement on the speed of hierarchical clustering task
• Minor bug fixes

9.0.19.1213

...

• Plot multiple viewers in one session
• Data content can be selected from any data node in the same project
• Analysis steps are recorded in each viewer session, Undo/Redo is enabled
• Plot types are2D scatterplot, 3D scatterplot, feature histogram, feature profiles
• Tables and text boxes can be added in data viewer
• Data node used for axes can be different from data node used for rendering

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1231

• Added heatmap plot type in data viewer, hierarchical cluster report is in data viewer
• Added pie chart on visualizing categorical sample/cell annotation
• Added Harmony algorithm for data transformation
• Added Scran normalization method
• Added Seurat 3 integration task
• Added more options on descriptive statistics task
• Added filtering capability on task management page
• Added ability to perform biological interpretation on miRNA data
• Added similarity matrix task on bulk RNA count matrix data node
• Added correlation section on task menu and move sample correction, correlation analysis under this menu
• Added function to import count matrix to allow import multiple files
• Added function to use sample name to split attribute on single cell data node
• Improved text importer to handle text file generated from R which has the first column shifted
• Improved speed on data viewer
• Improved volcano plot display
• Improved filter feature task dialog speed and added filter based on feature meta data
• Changed the default calculation on features in descriptive statistics dialog
• Changed single cell QA/QC plot to display 4 plots by default
• Changed DESeq2 only normalization report not using per million scale
• Changed the per million normalization using the sum of input count instead of aligned read counts
• Removed the log transformation in tSNE, UMAP and graph-base clustering dialog to reduce confusion
• Minor bug fixes