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