Page History

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

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11.0.23.

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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
Added split sample option in single cell QA/QC task
Improvement on memory usage for variant validation task
Minor bug fixes

Latest docker image: registry.partek.com/rtw:23.0720.334

10.0.23.0531

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: registry.partek.com/rtw:23.0531.320

10.0.23.0519

Minor bug fixes

Latest docker image: registry.partek.com/rtw:23.0519.317

10.0.23.0425

Minor bug fixes

Latest docker image: registry.partek.com/rtw:23.0425.313

10.0.23.0414

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: registry.partek.com/rtw:23.0414.312

10.0.23.0326

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: registry.partek.com/rtw:23.0326.310

10.0.23.0312

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: registry.partek.com/rtw:23.0312.310

10.0.23.0214

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: registry.partek.com/rtw:23.0214.305

10.0.23.0131

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: registry.partek.com/rtw:23.0131.304

10.0.23.0124

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

Latest docker image: registry.partek.com/rtw:23.0124.298

10.0.22.1204

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: registry.partek.com/rtw:22.1204.290

10.0.22.1111

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

0906

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