Partek
  • Overview
  • Partek Flow
    • Frequently Asked Questions
      • General
      • Visualization
      • Statistics
      • Biological Interpretation
      • How to cite Partek software
    • Quick Start Guide
    • Installation Guide
      • Minimum System Requirements
      • Single Cell Toolkit System Requirements
      • Single Node Installation
      • Single Node Amazon Web Services Deployment
      • Multi-Node Cluster Installation
      • Creating Restricted User Folders within the Partek Flow server
      • Updating Partek Flow
      • Uninstalling Partek Flow
      • Dependencies
      • Docker and Docker-compose
      • Java KeyStore and Certificates
      • Kubernetes
    • Live Training Event Recordings
      • Bulk RNA-Seq Analysis Training
      • Basic scRNA-Seq Analysis & Visualization Training
      • Advanced scRNA-Seq Data Analysis Training
      • Bulk RNA-Seq and ATAC-Seq Integration Training
      • Spatial Transcriptomics Data Analysis Training
      • scRNA and scATAC Data Integration Training
    • Tutorials
      • Creating and Analyzing a Project
        • Creating a New Project
        • The Metadata Tab
        • The Analyses Tab
        • The Log Tab
        • The Project Settings Tab
        • The Attachments Tab
        • Project Management
        • Importing a GEO / ENA project
      • Bulk RNA-Seq
        • Importing the tutorial data set
        • Adding sample attributes
        • Running pre-alignment QA/QC
        • Trimming bases and filtering reads
        • Aligning to a reference genome
        • Running post-alignment QA/QC
        • Quantifying to an annotation model
        • Filtering features
        • Normalizing counts
        • Exploring the data set with PCA
        • Performing differential expression analysis with DESeq2
        • Viewing DESeq2 results and creating a gene list
        • Viewing a dot plot for a gene
        • Visualizing gene expression in Chromosome view
        • Generating a hierarchical clustering heatmap
        • Performing biological interpretation
        • Saving and running a pipeline
      • Analyzing Single Cell RNA-Seq Data
      • Analyzing CITE-Seq Data
        • Importing Feature Barcoding Data
        • Data Processing
        • Dimensionality Reduction and Clustering
        • Classifying Cells
        • Differentially Expressed Proteins and Genes
      • 10x Genomics Visium Spatial Data Analysis
        • Start with pre-processed Space Ranger output files
        • Start with 10x Genomics Visium fastq files
        • Spatial data analysis steps
        • View tissue images
      • 10x Genomics Xenium Data Analysis
        • Import 10x Genomics Xenium Analyzer output
        • Process Xenium data
        • Perform Exploratory analysis
        • Make comparisons using Compute biomarkers and Biological interpretation
      • Single Cell RNA-Seq Analysis (Multiple Samples)
        • Getting started with the tutorial data set
        • Classify cells from multiple samples using t-SNE
        • Compare expression between cell types with multiple samples
      • Analyzing Single Cell ATAC-Seq data
      • Analyzing Illumina Infinium Methylation array data
      • NanoString CosMx Tutorial
        • Importing CosMx data
        • QA/QC, data processing, and dimension reduction
        • Cell typing
        • Classify subpopulations & differential expression analysis
    • User Manual
      • Interface
      • Importing Data
        • SFTP File Transfer Instructions
        • Import single cell data
        • Importing 10x Genomics Matrix Files
        • Importing and Demultiplexing Illumina BCL Files
        • Partek Flow Uploader for Ion Torrent
        • Importing 10x Genomics .bcl Files
        • Import a GEO / ENA project
      • Task Menu
        • Task actions
        • Data summary report
        • QA/QC
          • Pre-alignment QA/QC
          • ERCC Assessment
          • Post-alignment QA/QC
          • Coverage Report
          • Validate Variants
          • Feature distribution
          • Single-cell QA/QC
          • Cell barcode QA/QC
        • Pre-alignment tools
          • Trim bases
          • Trim adapters
          • Filter reads
          • Trim tags
        • Post-alignment tools
          • Filter alignments
          • Convert alignments to unaligned reads
          • Combine alignments
          • Deduplicate UMIs
          • Downscale alignments
        • Annotation/Metadata
          • Annotate cells
          • Annotation report
          • Publish cell attributes to project
          • Attribute report
          • Annotate Visium image
        • Pre-analysis tools
          • Generate group cell counts
          • Pool cells
          • Split matrix
          • Hashtag demultiplexing
          • Merge matrices
          • Descriptive statistics
          • Spot clean
        • Aligners
        • Quantification
          • Quantify to annotation model (Partek E/M)
          • Quantify to transcriptome (Cufflinks)
          • Quantify to reference (Partek E/M)
          • Quantify regions
          • HTSeq
          • Count feature barcodes
          • Salmon
        • Filtering
          • Filter features
          • Filter groups (samples or cells)
          • Filter barcodes
          • Split by attribute
          • Downsample Cells
        • Normalization and scaling
          • Impute low expression
          • Impute missing values
          • Normalization
          • Normalize to baseline
          • Normalize to housekeeping genes
          • Scran deconvolution
          • SCTransform
          • TF-IDF normalization
        • Batch removal
          • General linear model
          • Harmony
          • Seurat3 integration
        • Differential Analysis
          • GSA
          • ANOVA/LIMMA-trend/LIMMA-voom
          • Kruskal-Wallis
          • Detect alt-splicing (ANOVA)
          • DESeq2(R) vs DESeq2
          • Hurdle model
          • Compute biomarkers
          • Transcript Expression Analysis - Cuffdiff
          • Troubleshooting
        • Survival Analysis with Cox regression and Kaplan-Meier analysis - Partek Flow
        • Exploratory Analysis
          • Graph-based Clustering
          • K-means Clustering
          • Compare Clusters
          • PCA
          • t-SNE
          • UMAP
          • Hierarchical Clustering
          • AUCell
          • Find multimodal neighbors
          • SVD
          • CellPhoneDB
        • Trajectory Analysis
          • Trajectory Analysis (Monocle 2)
          • Trajectory Analysis (Monocle 3)
        • Variant Callers
          • SAMtools
          • FreeBayes
          • LoFreq
        • Variant Analysis
          • Fusion Gene Detection
          • Annotate Variants
          • Annotate Variants (SnpEff)
          • Annotate Variants (VEP)
          • Filter Variants
          • Summarize Cohort Mutations
          • Combine Variants
        • Copy Number Analysis (CNVkit)
        • Peak Callers (MACS2)
        • Peak analysis
          • Annotate Peaks
          • Filter peaks
          • Promoter sum matrix
        • Motif Detection
        • Metagenomics
          • Kraken
          • Alpha & beta diversity
          • Choose taxonomic level
        • 10x Genomics
          • Cell Ranger - Gene Expression
          • Cell Ranger - ATAC
          • Space Ranger
          • STARsolo
        • V(D)J Analysis
        • Biological Interpretation
          • Gene Set Enrichment
          • GSEA
        • Correlation
          • Correlation analysis
          • Sample Correlation
          • Similarity matrix
        • Export
        • Classification
        • Feature linkage analysis
      • Data Viewer
      • Visualizations
        • Chromosome View
          • Launching the Chromosome View
          • Navigating Through the View
          • Selecting Data Tracks for Visualization
          • Visualizing the Results Using Data Tracks
          • Annotating the Results
          • Customizing the View
        • Dot Plot
        • Volcano Plot
        • List Generator (Venn Diagram)
        • Sankey Plot
        • Transcription Start Site (TSS) Plot
        • Sources of variation plot
        • Interaction Plots
        • Correlation Plot
        • Pie Chart
        • Histograms
        • Heatmaps
        • PCA, UMAP and tSNE scatter plots
        • Stacked Violin Plot
      • Pipelines
        • Making a Pipeline
        • Running a Pipeline
        • Downloading and Sharing a Pipeline
        • Previewing a Pipeline
        • Deleting a Pipeline
        • Importing a Pipeline
      • Large File Viewer
      • Settings
        • Personal
          • My Profile
          • My Preferences
          • Forgot Password
        • System
          • System Information
          • System Preferences
          • LDAP Configuration
        • Components
          • Filter Management
          • Library File Management
            • Library File Management Settings
            • Library File Management Page
            • Selecting an Assembly
            • Library Files
            • Update Library Index
            • Creating an Assembly on the Library File Management Page
            • Adding Library Files on the Library File Management Page
            • Adding a Reference Sequence
            • Adding a Cytoband
            • Adding Reference Aligner Indexes
            • Adding a Gene Set
            • Adding a Variant Annotation Database
            • Adding a SnpEff Variant Database
            • Adding a Variant Effect Predictor (VEP) Database
            • Adding an Annotation Model
            • Adding Aligner Indexes Based on an Annotation Model
            • Adding Library Files from Within a Project
            • Microarray Library Files
            • Adding Prep kit
            • Removing Library Files
          • Option Set Management
          • Task Management
          • Pipeline managment
          • Lists
        • Access
          • User Management
          • Group Management
          • Licensing
          • Directory Permissions
          • Access Control Log
          • Failed Logins
          • Orphaned files
        • Usage
          • System Queue
          • System Resources
          • Usage Report
      • Server Management
        • Backing Up the Database
        • System Administrator Guide (Linux)
        • Diagnosing Issues
        • Moving Data
        • Partek Flow Worker Allocator
      • Enterprise Features and Toolkits
        • REST API
          • REST API Command List
      • Microarray Toolkit
        • Importing Custom Microarrays
      • Glossary
    • Webinars
    • Blog Posts
      • How to select the best single cell quality control thresholds
      • Cellular Differentiation Using Trajectory Analysis & Single Cell RNA-Seq Data
      • Spatial transcriptomics—what’s the big deal and why you should do it
      • Detecting differential gene expression in single cell RNA-Seq analysis
      • Batch remover for single cell data
      • How to perform single cell RNA sequencing: exploratory analysis
      • Single Cell Multiomics Analysis: Strategies for Integration
      • Pathway Analysis: ANOVA vs. Enrichment Analysis
      • Studying Immunotherapy with Multiomics: Simultaneous Measurement of Gene and Protein
      • How to Integrate ChIP-Seq and RNA-Seq Data
      • Enjoy Responsibly!
      • To Boldly Go…
      • Get to Know Your Cell
      • Aliens Among Us: How I Analyzed Non-Model Organism Data in Partek Flow
    • White Papers
      • Understanding Reads in RNA-Seq Analysis
      • RNA-Seq Quantification
      • Gene-specific Analysis
      • Gene Set ANOVA
      • Partek Flow Security
      • Single Cell Scaling
      • UMI Deduplication in Partek Flow
      • Mapping error statistics
    • Release Notes
      • Release Notes Archive - Partek Flow 10
  • Partek Genomics Suite
    • Installation Guide
      • Minimum System Requirements
      • Computer Host ID Retrieval
      • Node Locked Installation
        • Windows Installation
        • Macintosh Installation
      • Floating/Locked Floating Installation
        • Linux Installation
          • FlexNet Installation on Linux
        • Installing FlexNet on Windows
        • License Server FAQ's
        • Client Computer Connection to License Server
      • Uninstalling Partek Genomics Suite
      • Updating to Version 7.0
      • License Types
      • Installation FAQs
    • User Manual
      • Lists
        • Importing a text file list
        • Adding annotations to a gene list
        • Tasks available for a gene list
        • Starting with a list of genomic regions
        • Starting with a list of SNPs
        • Importing a BED file
        • Additional options for lists
      • Annotation
      • Hierarchical Clustering Analysis
      • Gene Ontology ANOVA
        • Implementation Details
        • Configuring the GO ANOVA Dialog
        • Performing GO ANOVA
        • GO ANOVA Output
        • GO ANOVA Visualisations
        • Recommended Filters
      • Visualizations
        • Dot Plot
        • Profile Plot
        • XY Plot / Bar Chart
        • Volcano Plot
        • Scatter Plot and MA Plot
        • Sort Rows by Prototype
        • Manhattan Plot
        • Violin Plot
      • Visualizing NGS Data
      • Chromosome View
      • Methylation Workflows
      • Trio/Duo Analysis
      • Association Analysis
      • LOH detection with an allele ratio spreadsheet
      • Import data from Agilent feature extraction software
      • Illumina GenomeStudio Plugin
        • Import gene expression data
        • Import Genotype Data
        • Export CNV data to Illumina GenomeStudio using Partek report plug-in
        • Import data from Illumina GenomeStudio using Partek plug-in
        • Export methylation data to Illumina GenomeStudio using Partek report plug-in
    • Tutorials
      • Gene Expression Analysis
        • Importing Affymetrix CEL files
        • Adding sample information
        • Exploring gene expression data
        • Identifying differentially expressed genes using ANOVA
        • Creating gene lists from ANOVA results
        • Performing hierarchical clustering
        • Adding gene annotations
      • Gene Expression Analysis with Batch Effects
        • Importing the data set
        • Adding an annotation link
        • Exploring the data set with PCA
        • Detect differentially expressed genes with ANOVA
        • Removing batch effects
        • Creating a gene list using the Venn Diagram
        • Hierarchical clustering using a gene list
        • GO enrichment using a gene list
      • Differential Methylation Analysis
        • Import and normalize methylation data
        • Annotate samples
        • Perform data quality analysis and quality control
        • Detect differentially methylated loci
        • Create a marker list
        • Filter loci with the interactive filter
        • Obtain methylation signatures
        • Visualize methylation at each locus
        • Perform gene set and pathway analysis
        • Detect differentially methylated CpG islands
        • Optional: Add UCSC CpG island annotations
        • Optional: Use MethylationEPIC for CNV analysis
        • Optional: Import a Partek Project from Genome Studio
      • Partek Pathway
        • Performing pathway enrichment
        • Analyzing pathway enrichment in Partek Genomics Suite
        • Analyzing pathway enrichment in Partek Pathway
      • Gene Ontology Enrichment
        • Open a zipped project
        • Perform GO enrichment analysis
      • RNA-Seq Analysis
        • Importing aligned reads
        • Adding sample attributes
        • RNA-Seq mRNA quantification
        • Detecting differential expression in RNA-Seq data
        • Creating a gene list with advanced options
        • Visualizing mapped reads with Chromosome View
        • Visualizing differential isoform expression
        • Gene Ontology (GO) Enrichment
        • Analyzing the unexplained regions spreadsheet
      • ChIP-Seq Analysis
        • Importing ChIP-Seq data
        • Quality control for ChIP-Seq samples
        • Detecting peaks and enriched regions in ChIP-Seq data
        • Creating a list of enriched regions
        • Identifying novel and known motifs
        • Finding nearest genomic features
        • Visualizing reads and enriched regions
      • Survival Analysis
        • Kaplan-Meier Survival Analysis
        • Cox Regression Analysis
      • Model Selection Tool
      • Copy Number Analysis
        • Importing Copy Number Data
        • Exploring the data with PCA
        • Creating Copy Number from Allele Intensities
        • Detecting regions with copy number variation
        • Creating a list of regions
        • Finding genes with copy number variation
        • Optional: Additional options for annotating regions
        • Optional: GC wave correction for Affymetrix CEL files
        • Optional: Integrating copy number with LOH and AsCN
      • Loss of Heterozygosity
      • Allele Specific Copy Number
      • Gene Expression - Aging Study
      • miRNA Expression and Integration with Gene Expression
        • Analyze differentially expressed miRNAs
        • Integrate miRNA and Gene Expression data
      • Promoter Tiling Array
      • Human Exon Array
        • Importing Human Exon Array
        • Gene-level Analysis of Exon Array
        • Alt-Splicing Analysis of Exon Array
      • NCBI GEO Importer
    • Webinars
    • White Papers
      • Allele Intensity Import
      • Allele-Specific Copy Number
      • Calculating Genotype Likelihoods
      • ChIP-Seq Peak Detection
      • Detect Regions of Significance
      • Genomic Segmentation
      • Loss of Heterozygosity Analysis
      • Motif Discovery Methods
      • Partek Genomics Suite Security
      • Reads in RNA-Seq
      • RNA-Seq Methods
      • Unpaired Copy Number Estimation
    • Release Notes
    • Version Updates
    • TeamViewer Instructions
  • Getting Help
    • TeamViewer Instructions
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On this page
  • 12.5.0
  • 12.4.3
  • 12.4.2
  • 12.4.0
  • 12.3.0
  • 12.2.0
  • 12.1.0
  • 12.0.1
  • 12.0.0
  • 11.0.24.0604
  • 11.0.24.0414
  • 11.0.24.0325
  • 11.0.24.0317
  • 11.0.24.0311
  • 11.0.24.0226
  • 11.0.24.0204
  • 11.0.24.0102
  • 11.0.23.1204
  • 11.0.23.1105
  • 11.0.23.1023
  • 11.0.23.1009
  • 11.0.23.0918
  • Additional Assistance
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  1. Partek Flow

Release Notes

PreviousMapping error statisticsNextRelease Notes Archive - Partek Flow 10

Last updated 4 days ago

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

12.5.0

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

  • Added last login to user usage report

  • 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

Latest docker image: public.ecr.aws/partek-flow/rtw:12.5.0

12.4.3

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

  • Fixed issue with filtering being reflected in tissue images

  • Fixed issue with batch effect correction error

Latest docker image: public.ecr.aws/partek-flow/rtw:12.4.3

12.4.2

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

12.4.0

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

  • Fixed an issue where the SCTransform step in Seurat fails due to total size of an export exceeding the maximum allowed size.

  • 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

Latest docker image: public.ecr.aws/partek-flow/rtw:12.4.0

12.3.0

Release date: November 14, 2024

  • Improved 'rds' Seurat object name to be case insensitive

  • Transitioned the help documentation to Gitbook and added new data type tutorials

  • Added support to analyze Illumina methylation array data: Infinium HumanMethylation450K, Infinium MethylationEPIC v1.0, and Infinium Methylation Screening Array

  • Minor bug fixes

Latest docker image: public.ecr.aws/partek-flow/rtw:12.3.0

12.2.0

Release date: October 10, 2024

  • Minor bug fixes

12.1.0

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

12.0.1

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

12.0.0

  • 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

  • Updated default aligner settings to use the whole genome index as default

  • Additional sorting features added to the CellPhoneDB task

  • Minor bug fixes

11.0.24.0604

  • 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

  • Added support to import Seurat 5 object

  • 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

Latest docker image: registry.partek.com/rtw:24.0529.62

11.0.24.0414

  • 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

  • Improved file browser when specify a location and click go button, it will scroll to the location on the left panel

  • Moved all tasks in Peak analysis section to Region analysis section

  • Minor bug fixes

Latest docker image: registry.partek.com/rtw:24.0414.55

11.0.24.0325

  • Added more options for variant filter by fields

  • Minor bug fixes

Latest docker image: registry.partek.com/rtw:24.0325.52

11.0.24.0317

  • 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

11.0.24.0311

  • 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

11.0.24.0226

  • 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

  • Minor bug fixes

Latest docker image: registry.partek.com/rtw:24.0301.39

11.0.24.0204

  • 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

  • Added Poisson regression and Negative binomial regression as options in the Differential analysis task

  • Minor bug fixes

Latest docker image: registry.partek.com/rtw:24.0204.33

11.0.24.0102

  • 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

  • Updated FreeBayes to v1.3.6

  • 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

Latest docker image: registry.partek.com/rtw:24.0102.29

11.0.23.1204

  • 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

  • Fixed the Venn diagram issue on some of the browsers

  • Minor bug fixes

Latest docker image: registry.partek.com/rtw:23.1204.23

11.0.23.1105

  • 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

11.0.23.1023

  • Improved differential analysis report layout

  • Add impute missing value task

  • Minor bug fixes

Latest docker image: registry.partek.com/rtw:23.1023.14

11.0.23.1009

  • 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

11.0.23.0918

  • 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

Latest docker image: registry.partek.com/rtw:23.0918.1

Additional Assistance

Added a new visualization type,

Latest docker image:

Latest docker image:

Latest docker image:

If you need additional assistance, please visit to submit a help ticket or find phone numbers for regional support.

Installation Guide
Stacked Violin Plot
registry.partek.com/rtw:12.2.0
registry.partek.com/rtw:12.1.0
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Archived Release Notes -- Partek Flow 10
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