Partek Flow Documentation

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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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11.0.

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24.

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  • 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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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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