# Release Notes Archive - Partek Flow 10

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](https://help.partek.illumina.com/partek-flow/installation-guide).

## 10.0.23.0720

* 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](http://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](http://registry.partek.com/rtw:23.0531.320)

## 10.0.23.0519

* Minor bug fixes

Latest docker image: [registry.partek.com/rtw:23.0519.317](http://registry.partek.com/rtw:23.0519.317)

## 10.0.23.0425

* Minor bug fixes

Latest docker image: [registry.partek.com/rtw:23.0425.313](http://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](http://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](http://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](http://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](http://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](http://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](http://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](http://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

## 10.0.21.1116

* Sped up h5 file import
* Sped up transfer file process
* Added a new peak filter task
* Added log transformation on Scran deconvolution output data
* 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

## 10.0.21.1026

* Sped up sparse matrix import
* Added poscounts normalization method for DESeq2
* Added support on .gaf file as gene set library file format
* Minor bug fixes

## 10.0.21.1014

* 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
* Improved UMAP speed
* Improved task graph drawing speed
* Improved sra file importer
* Improved h5 importer to handle both 32bit and 64bit values
* Minor bug fixes

## 10.0.21.0929

* 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
* Added weighted nearest neighbor algorithm for multimodal single cell datasets analysis
* Improved speed on user interface interaction
* Minor bug fixes

## 10.0.21.0912

* 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
* Improved post-alignment QA/QC speed
* 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

## 10.0.21.0816

* Added a function to allow manually drag\&drop to change the order of features/observations on heatmap
* Minor bug fixes

## 10.0.21.0801

* 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
* Minor bug fixes

## 10.0.21.0723

* Updated bioproject download link based on the changes on ENA website
* Minor bug fixes

## 10.0.21.0718

* Added function to display both Ensembl gene ID and gene name in differential analysis report
* Improvement on interface response
* Minor bug fixes

## 10.0.21.0707

* 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
* Added function to display both Ensembl gene ID and gene name in data viewer table
* 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

## 10.0.21.0621

* 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 more functions on metagenomics data analysis
* Added STAR fusion function
* Minor bug fixes

## 10.0.21.0602

* 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
* Improved hierarchical clustering visualization – allow user to manually adjust dendrogram size
* 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

## 10.0.21.0509

* 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
* Improved the Seurat3 integration task
* Enable both Monocle 2 and Monocle 3 in trajectory analysis
* Added download options for mm39 assembly library files
* Minor bug fixes

## 10.0.21.0411

* 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

## 10.0.21.0328

* Added HTSeq quantification method to Microarray data analysis
* Added BWA method on ERCC in pre-alignment QA/QC
* Added project statistics information on homepage
* Improvement Monocle 3 (trajectory analysis) to automatically detect the input data is in log scale or not
* Minor bug fixes

## 10.0.21.0302

* 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 more options in usage report
* Changed the graph-based clustering nearest neighbor type default from KNN to NN-Descent
* Improvement on interface
* Minor bug fixes

## 10.0.21.0201

* Added publish cell attributes to project task
* Scatterplot selection labeling is turned off by default
* Minor bug fixes

## 10.0.21.0117

* Added more options to generate usage report
* Added more configuration options in BWA-MEM
* Added download to the user management table
* Minor bug fixes

## 10.0.20.1231

* 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
* Added Scran normalization method
* 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