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      • Creating and Analyzing a Project
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        • Importing the tutorial data set
        • Adding sample attributes
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        • Quantifying to an annotation model
        • Filtering features
        • Normalizing counts
        • Exploring the data set with PCA
        • Performing differential expression analysis with DESeq2
        • Viewing DESeq2 results and creating a gene list
        • Viewing a dot plot for a gene
        • Visualizing gene expression in Chromosome view
        • Generating a hierarchical clustering heatmap
        • Performing biological interpretation
        • Saving and running a pipeline
      • Analyzing Single Cell RNA-Seq Data
      • Analyzing CITE-Seq Data
        • Importing Feature Barcoding Data
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      • 10x Genomics Visium Spatial Data Analysis
        • Start with pre-processed Space Ranger output files
        • Start with 10x Genomics Visium fastq files
        • Spatial data analysis steps
        • View tissue images
      • 10x Genomics Xenium Data Analysis
        • Import 10x Genomics Xenium Analyzer output
        • Process Xenium data
        • Perform Exploratory analysis
        • Make comparisons using Compute biomarkers and Biological interpretation
      • Single Cell RNA-Seq Analysis (Multiple Samples)
        • Getting started with the tutorial data set
        • Classify cells from multiple samples using t-SNE
        • Compare expression between cell types with multiple samples
      • Analyzing Single Cell ATAC-Seq data
      • Analyzing Illumina Infinium Methylation array data
      • NanoString CosMx Tutorial
        • Importing CosMx data
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    • User Manual
      • Interface
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      • Task Menu
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        • Copy Number Analysis (CNVkit)
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      • Data Viewer
      • Visualizations
        • Chromosome View
          • Launching the Chromosome View
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          • Selecting Data Tracks for Visualization
          • Visualizing the Results Using Data Tracks
          • Annotating the Results
          • Customizing the View
        • Dot Plot
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        • Transcription Start Site (TSS) Plot
        • Sources of variation plot
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        • Stacked Violin Plot
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      • How to select the best single cell quality control thresholds
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      • Spatial transcriptomics—what’s the big deal and why you should do it
      • Detecting differential gene expression in single cell RNA-Seq analysis
      • Batch remover for single cell data
      • How to perform single cell RNA sequencing: exploratory analysis
      • Single Cell Multiomics Analysis: Strategies for Integration
      • Pathway Analysis: ANOVA vs. Enrichment Analysis
      • Studying Immunotherapy with Multiomics: Simultaneous Measurement of Gene and Protein
      • How to Integrate ChIP-Seq and RNA-Seq Data
      • Enjoy Responsibly!
      • To Boldly Go…
      • Get to Know Your Cell
      • Aliens Among Us: How I Analyzed Non-Model Organism Data in Partek Flow
    • White Papers
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      • Partek Flow Security
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      • Mapping error statistics
    • Release Notes
      • Release Notes Archive - Partek Flow 10
  • Partek Genomics Suite
    • Installation Guide
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      • Computer Host ID Retrieval
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        • Import gene expression data
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    • Tutorials
      • Gene Expression Analysis
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        • Importing the data set
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        • Exploring the data set with PCA
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        • Removing batch effects
        • Creating a gene list using the Venn Diagram
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      • Differential Methylation Analysis
        • Import and normalize methylation data
        • Annotate samples
        • Perform data quality analysis and quality control
        • Detect differentially methylated loci
        • Create a marker list
        • Filter loci with the interactive filter
        • Obtain methylation signatures
        • Visualize methylation at each locus
        • Perform gene set and pathway analysis
        • Detect differentially methylated CpG islands
        • Optional: Add UCSC CpG island annotations
        • Optional: Use MethylationEPIC for CNV analysis
        • Optional: Import a Partek Project from Genome Studio
      • Partek Pathway
        • Performing pathway enrichment
        • Analyzing pathway enrichment in Partek Genomics Suite
        • Analyzing pathway enrichment in Partek Pathway
      • Gene Ontology Enrichment
        • Open a zipped project
        • Perform GO enrichment analysis
      • RNA-Seq Analysis
        • Importing aligned reads
        • Adding sample attributes
        • RNA-Seq mRNA quantification
        • Detecting differential expression in RNA-Seq data
        • Creating a gene list with advanced options
        • Visualizing mapped reads with Chromosome View
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        • Gene Ontology (GO) Enrichment
        • Analyzing the unexplained regions spreadsheet
      • ChIP-Seq Analysis
        • Importing ChIP-Seq data
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        • Detecting peaks and enriched regions in ChIP-Seq data
        • Creating a list of enriched regions
        • Identifying novel and known motifs
        • Finding nearest genomic features
        • Visualizing reads and enriched regions
      • Survival Analysis
        • Kaplan-Meier Survival Analysis
        • Cox Regression Analysis
      • Model Selection Tool
      • Copy Number Analysis
        • Importing Copy Number Data
        • Exploring the data with PCA
        • Creating Copy Number from Allele Intensities
        • Detecting regions with copy number variation
        • Creating a list of regions
        • Finding genes with copy number variation
        • Optional: Additional options for annotating regions
        • Optional: GC wave correction for Affymetrix CEL files
        • Optional: Integrating copy number with LOH and AsCN
      • Loss of Heterozygosity
      • Allele Specific Copy Number
      • Gene Expression - Aging Study
      • miRNA Expression and Integration with Gene Expression
        • Analyze differentially expressed miRNAs
        • Integrate miRNA and Gene Expression data
      • Promoter Tiling Array
      • Human Exon Array
        • Importing Human Exon Array
        • Gene-level Analysis of Exon Array
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    • Webinars
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      • Allele Intensity Import
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      • Partek Genomics Suite Security
      • Reads in RNA-Seq
      • RNA-Seq Methods
      • Unpaired Copy Number Estimation
    • Release Notes
    • Version Updates
    • TeamViewer Instructions
  • Getting Help
    • TeamViewer Instructions
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  1. Partek Flow
  2. Release Notes

Release Notes Archive - Partek Flow 10

PreviousRelease NotesNextPartek Genomics Suite

Last updated 7 months ago

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 .

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:

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:

10.0.23.0519

  • Minor bug fixes

10.0.23.0425

  • Minor bug fixes

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

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

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

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

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

10.0.23.0124

  • Improved the I/O performance on the coverage report task

  • Minor bug fixes

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

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

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