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

12.2.0

Release date: October 10, 2024

• Minor bug fixes

Latest docker image: registry.partek.com/rtw:12.2.0

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• 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

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Release date: September 6, 2024

• Improved monocle 3 dialog by adding an option to set the number of nearest neighbors
• Venn Diagram set-up allows user option to match gene identifiers in either case-sensitive or case-insensitive mode
• Minor bug fixes

Latest docker image: registry.partek.com/rtw:12.1.0

12.0.1

Release date: July 12, 2024

• Bug fix: Data import of h5 or sparse matrix data may be affected when cell or feature filtering is enabled. We suggest reimporting this data type if these data types were imported between June 24, 2024 and July 11, 2024.
• Import of Alamar Bioscience proteomics data output in .csv format supported
• Support for Visium HD, 8uM and 16uM

Latest docker image: registry.partek.com/rtw:12.0.1

12.0.0

• A new look and feel with updated typography and icons, but the same functionality
• Improved sparse matrix import for speed
• Improved CosMx import for file compatibility
• Updated default aligner settings to use the whole genome index as default
• Additional sorting features added to the CellPhoneDB task
• Minor bug fixes

Latest docker image: registry.partek.com/rtw:12.0.0

11.0.24.0604

• Use multiple colors for a numeric variable to color the scatter plot
• Added Normalization task option to use a numeric attribute to divide or subtract from data
• Leiden algorithm option added to the graph-based clustering task
• Added support to import Seurat 5 object
• Added support to import Seurat object saved as .qs format
• Added filter feature option in SVD task
• Ability to specify multiple urls during fastq file import 
• Improved filter based on GSEA enrichment score dialog
• Minor bug fixes 

Latest docker image: registry.partek.com/rtw:24.0529.62

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
• 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

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