Release Notes Archive - Partek Flow 10
Last updated
Last updated
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 .
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
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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
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Minor bug fixes
Minor bug fixes
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
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
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
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
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
Improved the I/O performance on the coverage report task
Minor bug fixes
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
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
Minor bug fixes
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
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
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
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
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
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
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
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
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
Minor bug fixes
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
Improved the speed on sctransform task
Minor bug fixes
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
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
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
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
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
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
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
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
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
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
Minor bug fixes
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
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
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
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
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
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
Improvement Monocle 3 (trajectory analysis) to automatically detect the input data is in log scale or not
Minor bug fixes
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
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
Minor bug fixes
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
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