Flow Documentation

Partek Flow Documentation

Page tree
Skip to end of metadata
Go to start of metadata

You are viewing an old version of this page. View the current version.

Compare with Current View Page History

« Previous Version 5 Next »

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.

10.0.21.1116

  • 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


  • No labels