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

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12.0.

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• Added option to report down regulated genes (negative biomarkers) for each cluster in compute biomarkers 
• Added option to specify input data is linear or log scale
• Improvement on memory usage for variant validation task
• Minor bug fixes 

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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:2312.07200.3340

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11.0.

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24.

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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 registry.partek.com/rtw:2324.05310529.32062

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11.0.

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24.

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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 registry.partek.com/rtw:2324.05190414.31755

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11.0.

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24.

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0325

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

Latest docker image: registry registry.partek.com/rtw:2324.04250325.31352

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11.0.

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24.

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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 registry.partek.com/rtw:2324.04140317.31249

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11.0.

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24.

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0311

• Improved gene set enrichment analysis by adding feature identifier selector
• Improved data import to set the most recently opened directory as the default directory 
• Upgraded Cutadapt to version 4.2
• 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 registry.partek.com/rtw:2324.03260311.31045

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11.0.

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24.

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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 registry.partek.com/rtw:2324.03120301.31039

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11.0.

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24.

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0204

• Added rich factor in enrichment analysis report
• Added function to download gene lists in biological interpretation reports
• Improved Violin plot to have different Max on Y-axis in different groupslong 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 registry.partek.com/rtw:2324.02140204.30533

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11.0.

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24.

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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 registry.partek.com/rtw:2324.01310102.30429

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11.0.23.

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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:23.01241204.29823

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11.0.

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23.

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• Added an importer for Parse Biosciences single cell count sparse matrix file format
• Allowed the use of a feature list summary score to select cells, the score can be published to project level from the data viewer
• Switched the default feature scaling setting to standardize for a bubble map
• Changed the default settings to compute biomarkers for both graph-based clustering and K-means clustering dialogs
• Allowed the export of data as matrix from the heatmap viewer
• Minor bug fixes

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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:2223.12041105.29016

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11.0.

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23.

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• Bug fixes

10.0.22.1107

• Upgraded 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

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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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