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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 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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