Release Notes

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

12.7.0

Release date: June 17, 2025

Performance Improvements

• Faster Session Loading: Enhanced speed performance for loading data viewer sessions.

• Optimized File Imports:

  • Improved import handling for public database files and .h5ad files.

  • Updated memory prediction for CosMx file imports to better accommodate large datasets.

Analysis & Task Updates

• Differential Expression:

  • Updated the backing component for the differential expression report table.

  • Fixed issues with Poisson and Negative Binomial regression tasks.

  • The DESeq2 task now runs only on normalized data nodes that include effective library sizes.

• 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.

Data Management Fixes

• 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.

• Updated reported quota disk usage for improved accuracy.

Library Updates

• Upgraded the HDF5 C++ library to version 1.14.6.

Latest docker image: public.ecr.aws/partek-flow/rtw:12.7.0

12.6.1

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

12.6.0

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

• Fixed issue with empty column header for the biomarker table in Data viewer

• 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

Latest docker image: public.ecr.aws/partek-flow/rtw:12.6.0

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

• Added a new visualization type, Stacked Violin Plot

• 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

Latest docker image: registry.partek.com/rtw:12.2.0

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

Latest docker image: registry.partek.com/rtw:12.1.0

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

Latest docker image: registry.partek.com/rtw:12.0.0

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

Archived Release Notes -- Partek Flow 10

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