To install or upgrade to the latest version of Partek Flow software, follow the directions outlined in the Installation Guide.
Release date: November 18, 2025
Improved Normalization task runtime
Made Volcano plot icon only available on the contrast stats section of differential analysis report
Improved Filter features task and fixed issue filtering differentially expressed genes from a saved gene list with more than 500 entries at once
Updated Tomcat
Fixed issue exporting UMAP data node as .h5 file
Fixed issue importing CosMx data
Fixed issue with using Venn diagram list to filter differential analysis node
Latest docker image: public.ecr.aws/partek-flow/rtw:12.9.0
Release date: October 3, 2025
Fixed an issue related to gene filtering
Latest docker image: public.ecr.aws/partek-flow/rtw:12.8.2
Release date: August 28, 2025
Differential analysis for ANOVA, Limma, and DESeq2
Enabled "Report p-values for effects" by default to automatically report Ratio and Log2Ratio for quantitative factors.
Partial correlation will be set to Yes by default.
Data loaders
Updated enumerating spatial transcripts.
Improved first Data viewer session startup loading time.
EULA page: Updated software terms and conditions link.
Differential expression: Removed the hsql database as the backing component for all DE report tables and replaced it with using flow_table.
Visualize differentially expressed genes: Improved tables backing component to match Differential analysis report and Data viewer.
Optimized File Imports: Improved CosMx image importer to ignore files that start with "."
Latest docker image: public.ecr.aws/partek-flow/rtw:12.8.0
Release date: June 17, 2025
Faster Session Loading: Enhanced speed performance for loading data viewer sessions.
Optimized File Imports:
Improved import handling for public database files and .h5ad files.
Differential Expression:
Updated the backing component for the differential expression report table.
Fixed issues with Poisson and Negative Binomial regression tasks.
Resolved an issue with the cell annotation task failing after matrix filtering.
Fixed a bug preventing the Trim Adapters task node from opening.
Corrected sorting behavior on the Transfer File page to sort by last modified date.
Upgraded the HDF5 C++ library to version 1.14.6.
Latest docker image: public.ecr.aws/partek-flow/rtw:12.7.0
Release date: May 23, 2025
Fixed issue with batch effect correction using general linear model task
Latest docker image: public.ecr.aws/partek-flow/rtw:12.6.1
Release date: May 1, 2025
Added function to change Task data node color independent from Result data node color via right-click
Added Wilcoxon differential analysis model
Renamed internal administrator Group to Illumina and updated user administrator roles including "edit user" functions
Latest docker image: public.ecr.aws/partek-flow/rtw:12.6.0
Release date: March 24, 2025
Added Statistics classification task for logistic regression models, specifically to support proteomics use cases
Removed icons no longer used on scRNA normalization report
Updated font to match Illumina standard guidelines
Latest docker image: public.ecr.aws/partek-flow/rtw:12.5.0
Release date: February 27, 2025
Improved speed performance and related issues with importing single cell data
Fixed issues with creating a project from data nodes and downloading data from result nodes
Fixed issue with TF-IDF normalization
Latest docker image: public.ecr.aws/partek-flow/rtw:12.4.3
Release date: February 12, 2025
Added a new import option for a Feature list which allows users to explore a list of identified genes in analyses, like KEGG pathway gene set enrichment
Fixed an issue with outputs for Filtering observations which was affecting downstream tasks
Fixed issues with K-means clustering and Classify cells task
Latest docker image: public.ecr.aws/partek-flow/rtw:12.4.2
Release date: February 4, 2025
Fixed an issue causing failures with Cell Ranger and Space Ranger tasks due to broken symlinks
Fixed an issue where the Classify Cell Type task failed on human data
Fixed an issue where Scatterplots disappear when Groupings are highlighted by an attribute
Latest docker image: public.ecr.aws/partek-flow/rtw:12.4.0
Release date: November 14, 2024
Added a new visualization type,
Improved 'rds' Seurat object name to be case insensitive
Transitioned the help documentation to Gitbook and added new data type tutorials
Latest docker image: public.ecr.aws/partek-flow/rtw:12.3.0
Release date: October 10, 2024
Minor bug fixes
Latest docker image:
Release date: September 6, 2024
Improved monocle 3 dialog by adding an option to set the number of nearest neighbors
Venn Diagram set-up allows user option to match gene identifiers in either case-sensitive or case-insensitive mode
Minor bug fixes
Latest docker image:
Release date: July 12, 2024
Bug fix: Data import of h5 or sparse matrix data may be affected when cell or feature filtering is enabled. We suggest reimporting this data type if these data types were imported between June 24, 2024 and July 11, 2024.
Import of Alamar Bioscience proteomics data output in .csv format supported
Support for Visium HD, 8uM and 16uM
Latest docker image: registry.partek.com/rtw:12.0.1
A new look and feel with updated typography and icons, but the same functionality
Improved sparse matrix import for speed
Improved CosMx import for file compatibility
Latest docker image:
Use multiple colors for a numeric variable to color the scatter plot
Added Normalization task option to use a numeric attribute to divide or subtract from data
Leiden algorithm option added to the graph-based clustering task
Latest docker image: registry.partek.com/rtw:24.0529.62
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
Latest docker image: registry.partek.com/rtw:24.0414.55
Added more options for variant filter by fields
Minor bug fixes
Latest docker image: registry.partek.com/rtw:24.0325.52
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
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
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
Latest docker image: registry.partek.com/rtw:24.0301.39
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
Latest docker image: registry.partek.com/rtw:24.0204.33
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
Latest docker image: registry.partek.com/rtw:24.0102.29
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
Latest docker image: registry.partek.com/rtw:23.1204.23
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
Improved differential analysis report layout
Add impute missing value task
Minor bug fixes
Latest docker image: registry.partek.com/rtw:23.1023.14
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
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
Latest docker image: registry.partek.com/rtw:23.0918.1
If you need additional assistance, please visit to submit a help ticket or find phone numbers for regional support.
Fixed issue running Detect de novo motifs task
Fixed issue for DESeq2 output summary table compared to detailed reports
Point rendering: Improved rendering for 2D scatterplot so that points with a higher expression level are moved to the front.
Updated memory prediction for CosMx file imports to better accommodate large datasets.
Clustering:
The Leiden graph-based clustering task now supports a lower number of iterations per random start (default set to 2).
Correlation Across Assays:
Now filters out null values to improve result accuracy.
Principal Component Analysis (PCA):
Fixed column label issues in the PCA component loadings table.
Fixed issue with Gene set enrichment task pathway not showing color
Improved performance for Volcano plot feature dragging
Improved UI for allotted width in the Significance threshold slider used in the Volcano plot
Fixed issue for CellPhoneDB task after filtering
Made security vulnerability improvements and updated python2 to python3 dependency
Fixed issue for Monocle3 Trajectory analysis memory issue
Updated import for H5AD, file permission issues, and importing large unfiltered sparse matrix files
Updated Seurat object import so that all metadata fields in Seurat object can be selected for sample ID
Updated library size format entries for annotation files during Quantification
Fixed issue for missing Chromosome view option on filtered peak data node
Fixed issue with Single cell QA/QC task performance downstream of another observation filter
Fixed issue with creating a project from a filtered sample output data node
Improved Leiden Graph-based clustering performance
Updated "Contact us" to direct to Illumina support
Fixed CellPhoneDB add annotation option
Fixed mixed model ANOVA when random nested factor is added as the first factor in the model
Fixed CosMX import error
Updated disk storage allocation user roles
Fixed project role display
Fixed "Correlation across assays" data node selection
Fixed issue with opening "Annotate variant" nodes
Fixed issue for creating a project from filtered sample output data nodes
Fixed issue with Chromosome view icon missing in the differential expression report
Fixed issue with batch effect correction error
Fixed an issue causing the Correlation Plot is not generated for feature analyses
Fixed an issue where an import error message was not included in the error log
Fixed an issue where multiple ADAT files could not be imported into a project
Fixed an issue where system-wide attributes cause other features to not work as expected. Now, System-wide attributes are no longer available and Project-specific attributes are default
Fixed an issue where optional information in the Differential Methylation Report (e.g., Chromosome) is not properly displayed in the table
Fixed an issue where transferring projects with paired-end FASTQ files results in file name changes
Fixed an issue when clicking the ‘I don’t remember my username’ does not work as expected
Fixed an issue where the Quantification box-whisker plot does not change between gene level stats and transcript level report
Fixed an issue where filtering by gene score only works on one sample in a split sample configuration
Fixed an issue where the Imported Quantification data filter report is missing median, Q1, and Q3 data
Fixed an issue where the Top number of features cannot be set when scheduling a PCA task on a data node that is not yet generated
Fixed an issue resulting in an incorrect Salmon command prediction
Fixed scaling issues in the stacked violin plot when adjusting the Y-axis and when choosing “fit data” mode
Fixed an issue where multiple files are listed when selecting transcripts for a single CosMX image
Fixed an issue when downloading a Differential Genome Expression feature list and the ‘Include counts’ option is de-selected, the downloaded ZIP file cannot be opened
Minor bug fixes
Additional sorting features added to the CellPhoneDB task
Minor bug fixes
Added support to import Seurat object saved as .qs format
Added filter feature option in SVD task
Ability to specify multiple urls during fastq file import
Improved filter based on GSEA enrichment score dialog
Minor bug fixes
Moved all tasks in Peak analysis section to Region analysis section
Minor bug fixes
Minor bug fixes
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
Minor bug fixes
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
Includes performance optimizations and fixes for improved speed and usability of Partek Flow software. To upgrade to this version, please follow the steps outlined in our Installation Guide.
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:
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
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
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
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
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
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
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
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
Added annotate features task on single cell count data node
Added round normalization method
Added filter task on gene set enrichment report data node
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
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
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
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
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
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
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
Added TF_IDF normalization task
Added singular value decomposition task
Improved the Seurat3 integration computation on normalized with SCTransformed data by adding PrepSCTIntegration function
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
Added GSEA task for biological interpretation
Extend Cell ranger task to support custom assemblies
Improved Space ranger interface to be more intuitive
Sped up h5 file import
Sped up transfer file process
Added a new peak filter task
Added log transformation on Scran deconvolution output data
Sped up sparse matrix import
Added poscounts normalization method for DESeq2
Added support on .gaf file as gene set library file format
Added feature to allow search a list of gene names in volcano plot
Added S1 and SUM_MS values to INFO column in Pindel vcf files
Added Space ranger task in Flow for hg38, mm10 and hg38-mm10 assembly
Added Salmon algorithm to compute gene count from fastq files
Added Garnett cell type classification function
Added support on import and export of h5ad file format on scRNA-seq project
Improved PCA dialog when there is only one sample in the project, no need to select split sample option
Improved cell number and cell percentage descriptive statistics computation to give more options
Improved cell ranger functions to handle CITE-seq data
Added a function to allow manually drag&drop to change the order of features/observations on heatmap
Minor bug fixes
Improvement Kraken on handling samples with multiple files
Added report transcript assemblers option in HISAT2
Added download option on multiple fastq/bam files associated with one sample to allow download one merged file fastq/bam per sample
Updated bioproject download link based on the changes on ENA website
Minor bug fixes
Added function to display both Ensembl gene ID and gene name in differential analysis report
Improvement on interface response
Minor bug fixes
Added Flow version in each task details
Allow to change group order by drag and drop directly on the axis on scatter plot
Added re-order mode in heatmap to allow to drag and drop observation/feature labels to swap
Improve 10X Genomics Visium image annotation to handle multiple samples
Added 10X Genomics Cellranger to handle scRNA-seq data from 10X Genomics on human, mouse and human-mouse assemblies
Improve PCA computation on memory usage on large datasets
Added a sample level box plot on the sctransform task report
Added Cell Ranger to process 10X Genomics fastq files and generate count matrix data on hg38, mm10 and hg38-mm10 references
Improved library file deletion function – list all projects that using the file
Added a feature of allowing manually type in a list of features to color in scatterplot
Added annotate Visium task to add tissue position and image information on 10X Genomics Visium data
Added compute biomarker as an independent task in addition to the subtask in any classification task
Added number of genes for up and down regulation separately in volcano plot
Annotate Visium task to add tissue position and image information on 10X Genomics Visium data
Minor bug fixes
Added HTSeq quantification method to Microarray data analysis
Added BWA method on ERCC in pre-alignment QA/QC
Added project statistics information on homepage
Upgrade trajectory analysis using monocle 3 algorithm
Added bubble map shortcut in data viewer
Added function to specify gene list in filter feature dialog without creating a list beforehand
Added publish cell attributes to project task
Scatterplot selection labeling is turned off by default
Minor bug fixes
Added more options to generate usage report
Added more configuration options in BWA-MEM
Added download to the user management table
Added heatmap plot type in data viewer, hierarchical cluster report is in data viewer
Added pie chart on visualizing categorical sample/cell annotation
Added Harmony algorithm for data transformation
Simplified the wording on the settings menu
Minor bug fixes
Minor bug fixes
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
Allowed the export of data as matrix from the heatmap viewer
Minor bug fixes
Minor bug fixes
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
Changed the default graph-based clustering resolution to 0.5
Reorganized the task menu, added Statistics section
Minor bug fixes
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
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
Minor bug fixes
Removed Shrimp aligner support
Minor bug fixes
Improved feature list creation after features selected on data viewer
Minor bug fixes
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
Added option to use gene name or gene ID to filter features based on gene list task
Added region length information on differential analysis report on regions
Improved creating factorial comparisons on differential analysis dialog
Added feature list creation function in data viewer on selected features
Minor bug fixes
Improved task graph drawing speed
Improved sra file importer
Improved h5 importer to handle both 32bit and 64bit values
Minor bug fixes
Improved speed on user interface interaction
Minor bug fixes
Improved heatmap export to allow entire data after zoom in
Changed TPM normalization method, remove scaling across sample step
Added 10X CellRager HDF5 file format option when download single cell data matrix data node
Added visualization on enrichment report
Minor bug fixes
Added support on .tsv file format as cell annotation file
Added more descriptive statistics to filter cell task report
Output STAR fusion in vcf format
Improved speed on interface and visualization
Minor bug fixes
Added STAR fusion function
Minor bug fixes
Removed log transformation section in PCA and hierarchical clustering dialogs
Added more options in the STAR configuration dialog
STAR aligner is upgraded to 2.7.8a
Added support on Seurat4 objects import (requires R version 4 and above)
Minor bug fixes
Enable both Monocle 2 and Monocle 3 in trajectory analysis
Added download options for mm39 assembly library files
Minor bug fixes
Minor bug fixes
Changed the graph-based clustering nearest neighbor type default from KNN to NN-Descent
Improvement on interface
Minor bug fixes
Added Seurat 3 integration task
Added more options on descriptive statistics task
Added filtering capability on task management page
Added ability to perform biological interpretation on miRNA data
Added similarity matrix task on bulk RNA count matrix data node
Added correlation section on task menu and move sample correction, correlation analysis under this menu
Added function to import count matrix to allow import multiple files
Added function to use sample name to split attribute on single cell data node
Improved text importer to handle text file generated from R which has the first column shifted
Improved speed on data viewer
Improved volcano plot display
Improved filter feature task dialog speed and added filter based on feature meta data
Changed the default calculation on features in descriptive statistics dialog
Changed single cell QA/QC plot to display 4 plots by default
Changed DESeq2 only normalization report not using per million scale
Changed the per million normalization using the sum of input count instead of aligned read counts
Removed the log transformation in tSNE, UMAP and graph-base clustering dialog to reduce confusion
Minor bug fixes