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