To install or upgrade to the latest version of Partek^® Flow^® software, follow the directions outlined in the Installation Guide.

10.0.22.1204

• Added importer for Parse Biosciences single cell count sparse matrix file format
• Allowed to use feature list summary score to select cells, the score can be published to project level from data viewer
• Changed the default feature scaling setting to standardize for bubble map
• Change the default to compute biomarkers for graph-based clustering and K-means clustering dialogs
• Allowed to export data as matrix from heatmap viewer
• Minor bug fixes
• Latest Docker image: registry.partek.com/rtw:22.1204.290

10.0.22.1111

• Bug fixes

10.0.22.1107

• Upgrade peak detection method to MACS 3.0
• Added leading edge genes generation in GSEA report details
• Improved speed and performance on UI
• Minor bug fixes

10.0.22.1023

• Improved the KEGG pathway image update with version number
• Added a function to allow any project level attributes as sample ID when creating project from a data node
• Added stretch to view point option on axes configuration for more efficient space in 2D plots
• Minor bug fixes

10.0.22.1003

• Added annotate features task on single cell count data node
• Added round normalization method
• Added filter task on gene set enrichment report data node
• Added LIMMA-trend and LIMMA VOOM method options in differential analysis
• Minor bug fixes

10.0.22.0828

• Improved the Data viewer interface to make it more user friendly and more flexible, added how-to video link in each dialog
• Improved the speed and memory efficiency for the Seurat3 integration task
• Improved TF-IDF normalization memory usage
• Improved import of scATAC count matrix to be more memory efficient
• Changed the classify tool by removing the data node selection step when using apply classifications 
• Changed the computation of median, Q1, Q3 on the Box & Whisker plot using a different method to match the descriptive statistics method
• Changed the default promoter regions to be up/down 1000bp from TSS for annotate regions
• Added function to save video for 3D scatterplot rotation
• Added import for VDJ annotation combined with gene expression data generated from the Cell Ranger pipeline
• Added support for Space Ranger 2.0 outputs
• Added a function to compute descriptive statistics on observations to use a list of features
• Added Spot clean task on Space ranger output data node
• Combined differential analysis methods into one task on the menu
• Minor bug fixes

10.0.22.0727

• Added a task to merge adjacent regions
• Added a function to remove data published in data repository
• Improved scATAC data import to be more efficient on RAM usage
• Allow user to select whether to display shrinkage plot on GSA nd hurdle model report in advanced option
• Changed the default graph-based clustering resolution to 0.5
• Reorganized the task menu, added Statistics section
• Minor bug fixes

10.0.22.0703

• Upgrade MACS to version 3.0.0a7
• Added a function to allow user to perform motif detection on quantify region report
• Added flexibility to allow user to define TSS, TTS regions when perform peak annotation
• Renamed the default quantify region task report data node as region counts
• Added compare region tasks to allow user to compare regions among samples
• Added promoter sum task for scATAC data analysis
• Added down scale alignment tasks on aligned data node
• Allow user to run gene set enrichment task on filtered gene count matrix data node
• Merged Gene set enrichment and pathway enrichment tasks into one to reduce confusion
• Changed the graph-based clustering default resolution setting from 1 to 0.5 
• Minor bug fixes

10.0.22.0524

• Added a function to allow user to create annotation model from the reference
• Added a function to allow user to create new annotation model by merging to existing annotation models
• Improved the user interface on differential analysis tasks
• Minor bug fixes

10.0.22.0428

• Fixed the refresh delay issue on library file management dialog 

10.0.22.0424

• Added sorting observations based numeric attribute function on heatmap
• Added a function to allow user to create a new assembly reference by providing sequence
• Added a function to allow user to create a new assembly reference by merging two existing assembly
• Added case insensitive option when filter features based on a list
• Improved the interface of generating heatmap and bubble map
• Improved list creating to handle leading and trailing white space in the list
• Added function to allow user access read only directory
• Minor bug fixes

10.0.22.0410

• Improved feature on generating filtered node operation on differential analysis report page, the page will not redirect automatically after clicking the button
• Changed some import task labels
• Minor bug fixes

10.0.22.0330

• Changed the order of Annotation models section in library file management page, Genomics library files tab
• Removed selecting files from local computer option, instead files need to be transferred to server to be used in tasks
• Improved the speed of UI
• Minor bug fixes

10.0.22.0321

• Bug fix on enrichment report visualization
• Bug fix on Seurat3 integration task excluding feature IDs with hyphen

10.0.22.0313

• Added option to allow features to be sorted based on a feature list in heatmap
• Allow to invoke WNN on SVD data node
• Minor bug fixes

10.0.22.0228

• Improved on handling big genome alignment like wheat
• Added classification summary report on Garnett classify cell type task
• Allow to sort heatmap samples/cells using numeric attributes
• Improved the speed on sctransform task
• Minor bug fixes

10.0.22.0213

• Added TF_IDF normalization task
• Added singular value decomposition task
• Improved the Seurat3 integration computation on normalized with SCTransformed data by adding PrepSCTIntegration function
• Changed the Seurat object importer, added convert Seurat to matrix task
• Removed Shrimp aligner support
• Minor bug fixes

10.0.22.0130

• Improved Flow homepage layout
• Improved the pipeline management page
• Minor bug fixes

10.0.22.0121

• Added sorting observations based numeric attribute function on heatmap
• Added gene labeling option in heatmap when use Ensembl annotation
• Added CellRanger ATAC wrapper
• Improved filter observation tasks to easily choose multiple subgroups from the same attribute
• Improved feature list creation after features selected on data viewer
• Minor bug fixes

10.0.22.0102

• Added GSEA task for biological interpretation
• Extend Cell ranger task to support custom assemblies
• Improved Space ranger interface to be more intuitive
• Upgraded GATK to version 4.2
• Removed standardization option in t-SNE dialog
• Added learning rate parameter in t-SNE advanced dialog
• Added function to allow to specify multiple levels in each comparison panel in non-parametric ANOVA and Welch's ANOVA task
• Minor bug fixes

2021 Archived Release Notes

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