View Source

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

10.0.22.1204

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

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

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

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

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