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.

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

10.0.23.0531

• Improved 2D scatterplot labeling up to 2000 selected points
• Added option for deselected point color to be the same as selected point color
• Minor bug fixes 

Latest docker image: registry.partek.com/rtw:23.0531.320

10.0.23.0519

• Minor bug fixes 

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

10.0.23.0425

• Minor bug fixes 

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

10.0.23.0414

• Added FDR adjusted p-value in the enrichment report
• Added a function to remove empty folders on the settings menu
• Improved the bar chart to display text attributes
• Improved single cell count matrix import to allow user to filter cells with low umi counts
• Simplified the wording on the settings menu
• Minor bug fixes 

Latest docker image: registry.partek.com/rtw:23.0414.312

10.0.23.0326

• Improved gene set enrichment analysis by adding feature identifier selector
• Improved data import to set the most recently opened directory as the default directory 
• Upgraded Cutadapt to version 4.2
• Minor bug fixes 

Latest docker image: registry.partek.com/rtw:23.0326.310

10.0.23.0312

• Added links to the number of genes to download gene list in biological interpretation report
• Added a filter task on differential analysis report data node to extend the flexibility
• Improved GSEA task to perform on attributes with more than 2 groups
• Upgraded Space Ranger to 2.0.1
• Minor bug fixes 

Latest docker image: registry.partek.com/rtw:23.0312.310

10.0.23.0214

• Added rich factor in enrichment analysis report
• Added function to download gene lists in biological interpretation reports
• Improved Violin plot to have different Max on Y-axis in different groups
• Minor bug fixes 

Latest docker image: registry.partek.com/rtw:23.0214.305

10.0.23.0131

• Added an optional t-statistic value output to the ANOVA report
• Added support for the Parse Bio SPLiT-Seq count matrix data format
• Allowed the Annotate feature task to be performed on count matrix data nodes
• Added Survival analysis task options
• Added function allowing the selection of cells based on a score from a list of genes 
• Added motif detection function to the gene list report in the RNA-Seq assay
• Added primary ID option to allow selection when there are two IDs in the file to import
• Added support for single sign-on
• Improved the transfer file function to not observe the time out setting
• Refined the import for single cell sparse matrix files (3 files per sample) to support multiple samples at one time
• Improved the Correlation analysis task to allow the user to search for specific features to perform correlation with all the features
• Optimized the default Volcano plot display
• Changed the default settings on a 2D scatterplot to fill the view
• Upgraded SCTransform v2
• Minor bug fixes 

Latest docker image: registry.partek.com/rtw:23.0131.304

10.0.23.0124

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

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

10.0.22.1204

• Added an importer for Parse Biosciences single cell count sparse matrix file format
• Allowed the use of a feature list summary score to select cells, the score can be published to project level from the data viewer
• Switched the default feature scaling setting to standardize for a bubble map
• Changed the default settings to compute biomarkers for both graph-based clustering and K-means clustering dialogs
• Allowed the export of data as matrix from the heatmap viewer
• Minor bug fixes

Latest Docker image: registry.partek.com/rtw:22.1204.290

10.0.22.1111

• Bug fixes

10.0.22.1107

• Upgraded peak detection method to MACS 3.0
• Added leading edge genes generation in GSEA report details
• Improved speed and performance on UI
• Minor bug fixes

10.0.22.1023

• Improved the KEGG pathway image update with version number
• Added a function to allow any project level attributes as sample ID when creating project from a data node
• Added stretch to view point option on axes configuration for more efficient space in 2D plots
• Minor bug fixes

10.0.22.1003

• Added annotate features task on single cell count data node
• Added round normalization method
• Added filter task on gene set enrichment report data node
• Added LIMMA-trend and LIMMA VOOM method options in differential analysis
• Minor bug fixes

10.0.22.0828

• Improved the Data viewer interface to make it more user friendly and more flexible, added how-to video link in each dialog
• Improved the speed and memory efficiency for the Seurat3 integration task
• Improved TF-IDF normalization memory usage
• Improved import of scATAC count matrix to be more memory efficient
• Changed the classify tool by removing the data node selection step when using apply classifications 
• Changed the computation of median, Q1, Q3 on the Box & Whisker plot using a different method to match the descriptive statistics method
• Changed the default promoter regions to be up/down 1000bp from TSS for annotate regions
• Added function to save video for 3D scatterplot rotation
• Added import for VDJ annotation combined with gene expression data generated from the Cell Ranger pipeline
• Added support for Space Ranger 2.0 outputs
• Added a function to compute descriptive statistics on observations to use a list of features
• Added Spot clean task on Space ranger output data node
• Combined differential analysis methods into one task on the menu
• Minor bug fixes

10.0.22.0727

• Added a task to merge adjacent regions
• Added a function to remove data published in data repository
• Improved scATAC data import to be more efficient on RAM usage
• Allow user to select whether to display shrinkage plot on GSA nd hurdle model report in advanced option
• Changed the default graph-based clustering resolution to 0.5
• Reorganized the task menu, added Statistics section
• Minor bug fixes

10.0.22.0703

• Upgrade MACS to version 3.0.0a7
• Added a function to allow user to perform motif detection on quantify region report
• Added flexibility to allow user to define TSS, TTS regions when perform peak annotation
• Renamed the default quantify region task report data node as region counts
• Added compare region tasks to allow user to compare regions among samples
• Added promoter sum task for scATAC data analysis
• Added down scale alignment tasks on aligned data node
• Allow user to run gene set enrichment task on filtered gene count matrix data node
• Merged Gene set enrichment and pathway enrichment tasks into one to reduce confusion
• Changed the graph-based clustering default resolution setting from 1 to 0.5 
• Minor bug fixes

10.0.22.0524

• Added a function to allow user to create annotation model from the reference
• Added a function to allow user to create new annotation model by merging to existing annotation models
• Improved the user interface on differential analysis tasks
• Minor bug fixes

10.0.22.0428

• Fixed the refresh delay issue on library file management dialog 

10.0.22.0424

• Added sorting observations based numeric attribute function on heatmap
• Added a function to allow user to create a new assembly reference by providing sequence
• Added a function to allow user to create a new assembly reference by merging two existing assembly
• Added case insensitive option when filter features based on a list
• Improved the interface of generating heatmap and bubble map
• Improved list creating to handle leading and trailing white space in the list
• Added function to allow user access read only directory
• Minor bug fixes

10.0.22.0410

• Improved feature on generating filtered node operation on differential analysis report page, the page will not redirect automatically after clicking the button
• Changed some import task labels
• Minor bug fixes

10.0.22.0330

• Changed the order of Annotation models section in library file management page, Genomics library files tab
• Removed selecting files from local computer option, instead files need to be transferred to server to be used in tasks
• Improved the speed of UI
• Minor bug fixes

10.0.22.0321

• Bug fix on enrichment report visualization
• Bug fix on Seurat3 integration task excluding feature IDs with hyphen

10.0.22.0313

• Added option to allow features to be sorted based on a feature list in heatmap
• Allow to invoke WNN on SVD data node
• Minor bug fixes

10.0.22.0228

• Improved on handling big genome alignment like wheat
• Added classification summary report on Garnett classify cell type task
• Allow to sort heatmap samples/cells using numeric attributes
• Improved the speed on sctransform task
• Minor bug fixes

10.0.22.0213

• Added TF_IDF normalization task
• Added singular value decomposition task
• Improved the Seurat3 integration computation on normalized with SCTransformed data by adding PrepSCTIntegration function
• Changed the Seurat object importer, added convert Seurat to matrix task
• Removed Shrimp aligner support
• Minor bug fixes

10.0.22.0130

• Improved Flow homepage layout
• Improved the pipeline management page
• Minor bug fixes

10.0.22.0121

• Added sorting observations based numeric attribute function on heatmap
• Added gene labeling option in heatmap when use Ensembl annotation
• Added CellRanger ATAC wrapper
• Improved filter observation tasks to easily choose multiple subgroups from the same attribute
• Improved feature list creation after features selected on data viewer
• Minor bug fixes

10.0.22.0102

• Added GSEA task for biological interpretation
• Extend Cell ranger task to support custom assemblies
• Improved Space ranger interface to be more intuitive
• Upgraded GATK to version 4.2
• Removed standardization option in t-SNE dialog
• Added learning rate parameter in t-SNE advanced dialog
• Added function to allow to specify multiple levels in each comparison panel in non-parametric ANOVA and Welch's ANOVA task
• Minor bug fixes

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