Partek Flow Documentation

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

  • Improved 2D scatterplot labeling up to 2000 selected points
  • Added option for deselected point color to be the same as selected point color
  • Minor bug fixes 

Latest docker image:

  • Minor bug fixes 

Latest docker image:

  • Minor bug fixes 

Latest docker image:

  • Added FDR adjusted p-value in the enrichment report
  • Added a function to remove empty folders on the settings menu
  • Improved the bar chart to display text attributes
  • Improved single cell count matrix import to allow user to filter cells with low umi counts
  • Simplified the wording on the settings menu
  • Minor bug fixes 

Latest docker image:

  • 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
  • Minor bug fixes 

Latest docker image:

  • Added links to the number of genes to download gene list in biological interpretation report
  • Added a filter task on differential analysis report data node to extend the flexibility
  • Improved GSEA task to perform on attributes with more than 2 groups
  • Upgraded Space Ranger to 2.0.1
  • Minor bug fixes 

Latest docker image:

  • 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 groups
  • Minor bug fixes 

Latest docker image:

  • Added an optional t-statistic value output to the ANOVA report
  • Added support for the Parse Bio SPLiT-Seq count matrix data format
  • Allowed the Annotate feature task to be performed on count matrix data nodes
  • Added Survival analysis task options
  • Added function allowing the selection of cells based on a score from a list of genes 
  • Added motif detection function to the gene list report in the RNA-Seq assay
  • Added primary ID option to allow selection when there are two IDs in the file to import
  • Added support for single sign-on
  • Improved the transfer file function to not observe the time out setting
  • Refined the import for single cell sparse matrix files (3 files per sample) to support multiple samples at one time
  • Improved the Correlation analysis task to allow the user to search for specific features to perform correlation with all the features
  • Optimized the default Volcano plot display
  • Changed the default settings on a 2D scatterplot to fill the view
  • Upgraded SCTransform v2
  • Minor bug fixes 

Latest docker image:

  • Improved the I/O performance on the coverage report task
  • Minor bug fixes

Latest docker image:

  • 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

Latest Docker image:

  • Bug fixes

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • Fixed the refresh delay issue on library file management dialog

  • 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

  • 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

  • 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

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

  • 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

  • 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

  • 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

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

  • 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

  • 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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