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

...

11.0.

...

24.

...

0414

...

• Added CellphoneDB task to analyze cell-cell communication process
• Added display transcripts location ability on 10X Genomics Xenium data visualization
• Improved trim adaptor task to be more memory efficient
• Changed the apply classifications task by removing the data node selection step
• 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 on 3D scatterplot rotation
• Added import for VDJ annotation combined with gene expression data generated from 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 function 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

• Improved file browser when specify a location and click go button, it will scroll to the location on the left panel
• Moved all tasks in Peak analysis section to Region analysis section
• Minor bug fixes 

Latest docker image: registry.partek.com/rtw:24.0414.55

11.0.24.0325

• Added more options for variant filter by fields
• Minor bug fixes 

Latest docker image: registry.partek.com/rtw:24.0325.52

11.0.24.0317

• Added hierarchical cluster analysis task to similarity matrix data node
• Added statistical analysis task to cell descriptive stats
• Minor bug fixes 

Latest docker image: registry.partek.com/rtw:24.0317.49

11.0.24.0311

• Improved convert Seurat to matrix dialog to allow to configure meta data
• Added more options in filter annotated peaks dialog
• Minor bug fixes 

Latest docker image: registry.partek.com/rtw:24.0311.45

11.0.24.0226

• Improved differential analysis report filter option on log2 ratio to allow user to specify a range to filter
• Improved Normalize to housekeeping genes dialog to display both gene ID and gene name
• Added data repository management on Settings page
• Minor bug fixes 

Latest docker image: registry.partek.com/rtw:24.0301.39

11.0.24.0204

• Added long reads aligner minimap2 and pbmm2
• Simplified the Data Viewer configuration dialogs
• Added Scree plot and component loadings table to the PCA report by default
• Added Poisson regression and Negative binomial regression as options in the Differential analysis task
• Minor bug fixes 

Latest docker image: registry.partek.com/rtw:24.0204.33

11.0.24.0102

• Automatically generate spatial report on analysis tab after spatial data import
• Added alt-splicing task option on Salmon's transcript count data node
• Added STARsolo task for 10x Genomics scRNA-seq data
• Updated FreeBayes to v1.3.6
• PCA task default feature filter method is changed to variance from vst 
• Filter peaks task is moved to Filtering section from Peak analysis section on the menu
• Make the enable/disable user account as separate privilege from add user account for admin
• Minor bug fixes 

Latest docker image: registry.partek.com/rtw:24.0102.29

11.0.23.1204

• Enabled MACS peak detection report visualizations in the Data viewer
• Improved the algorithm for the normalize to housekeeping genes task
• Added more gene annotation options in SNV task report
• Fixed the Venn diagram issue on some of the browsers
• Minor bug fixes 

Latest docker image: registry.partek.com/rtw:23.1204.23

11.0.23.1105

• Added search function in Help menu to directly search the content in documentation page
• Added option to choose a number of features to use in PCA computation
• Minor bug fixes 

Latest docker image: registry.partek.com/rtw:23.1105.16

11.0.23.1023

• Improved differential analysis report layout
• Add impute missing value task
• Minor bug fixes 

Latest docker image: registry.partek.com/rtw:23.1023.14

11.0.23.1009

• Improved pre-alignment QC report
• Fixed differential analysis report table download issue
• Minor bug fixes 

Latest docker image: registry.partek.com/rtw:23.1009.11

11.0.23.0918

• The user interface now boasts a modern appearance
• Enhanced the import wizard for greater intuitiveness and user-friendliness
• Added support for SomaLogic ADAT bulk protein data
• Improved the file browser for fast access to recent server uploads 
• Bolstered file protection to prevent accidental deletions when used by other projects
• Added support for the 10x Genomics Xenium platform 
• Introduced support for the Nanostring CosMx platform
• Added a new task for Correlation analysis between different assays
• Improved scatterplot selection with a handy painting mode 
• Added the ability to display a high resolution Visium image with a new Spatial imaging report task for quick viewing
• Added a manual alignment option for tissue image visualization 
• Streamlined the import process for multiple files per sample, e.g. import all 3 sparse matrix (feature-barcode-matrix) files per sample for all samples at one time 
• Added more available information on the Annotated region report
• Improved the Seurat object conversion to be more intuitive
• Added a more detailed report to the Adapter trimming task
• Creating pseudobulk data by pooling single cells has been made easier with increased functionality
• Optimized the differential analysis dialogs for improved usability 
• Changed the default normalization method for bulk RNA-Seq data to Median ratio (DESeq2)
• Improved the Detect fusions and Trim bases tasks to be more intuitive 
• Allowed the Single-cell QA/QC task to be performed on individual samples
• Minor bug fixes 

Latest docker image: registry.partek.com/rtw:23.0918.1

Archived Release Notes -- Partek Flow 10

...