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chevron_left Read quality control Known transcript quantification Differential expression Bioinformatics workflows Spliced read alignment Gene expression visualization chevron_right

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Partek Flow specifications


Unique identifier OMICS_15740
Name Partek Flow
Software type Pipeline/Workflow
Interface Graphical user interface
Restrictions to use License purchase required
Operating system Unix/Linux, Mac OS
License Commercial
Computer skills Medium
Stability Stable
Maintained Yes


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Partek Flow citations


A framework for the estimation of the proportion of true discoveries in single nucleotide variant detection studies for human data

PLoS One
PMCID: 5918994
PMID: 29694377
DOI: 10.1371/journal.pone.0196058

[…] and the author of this manuscript has the following competing interests: nik tuzov holds full time, paid employment at partek incorporated. the commercial software produced by partek incorporated (“partek flow” and “partek genomics suite”) was used extensively to obtain the results presented in the manuscript. this affiliation does not alter the author’s adherence to plos one policies […]


The striatal kinase DCLK3 produces neuroprotection against mutant huntingtin

PMCID: 5917821
PMID: 29534157
DOI: 10.1093/brain/awy057

[…] bc chip and sequenced on the ion proton system by ion pi ic 200 kit chemistry (200-bp read length; life technologies). the ion proton reads (fastq files) were imported into the rna-seq pipeline of partek flow software (v 4.0, partek inc), with hg19 as the reference genome. we identified genes differentially expressed between groups, by quantifying mapped reads with the partek e/m algorithm […]


Cathelicidin promotes inflammation by enabling binding of self RNA to cell surface scavenger receptors

Sci Rep
PMCID: 5838106
PMID: 29507358
DOI: 10.1038/s41598-018-22409-3

[…] sequencing. libraries were constructed using truseq stranded mrna library prepkits (illumina, san diego, ca) and run on a hiseq. 2500 instrument (illumina). raw data were analyzed using partek flow and partek genomics suite software v6.0.17.0319 to determine transcript abundance and differentially expressed genes between samples. gene ontology analysis was performed using the gene […]


Lung microRNA deregulation associated with impaired alveolarization in rats after intrauterine growth restriction

PLoS One
PMCID: 5747455
PMID: 29287116
DOI: 10.1371/journal.pone.0190445

[…] by using expression console software (affymetrix) to obtain raw data (cel files) and metrics for quality control. no apparent outliers were detected., specific mirna analysis involved use of partek flow v3.0 (partek inc., st. louis, mo). cel files were imported and normalized by robust multi-array averaging (rma). the mirna 4.0 chip contained probes for 490 rat pre-mirnas and 728 rat […]


Dual modulation of human hepatic zonation via canonical and non canonical Wnt pathways

PMCID: 5750478
PMID: 29244788
DOI: 10.1038/emm.2017.226

[…] cdna were assessed using a 2100 bioanalyzer (agilent technologies, santa clara, ca, usa). rna sequencing data are deposited at ncbi under accession code gse83990., rna-seq data were analyzed with partek flow version 4 (partek). raw sequencing reads were first trimmed from both ends with a quality score method (bases with a quality score of less than 20 were trimmed from both ends, and trimmed […]


Malaria parasite DNA harbouring vesicles activate cytosolic immune sensors

Nat Commun
PMCID: 5719353
PMID: 29215015
DOI: 10.1038/s41467-017-02083-1

[…] rna sequences were analyzed for quality control using fastqc and the torrent suite 3.4.1. output files (*.bam) were uploaded and aligned to the h. sapiens genome (hg19) using bowtie 2, using partek flow (partek incorporated, singapore). remaining unaligned reads were passed through for a second alignment with the p. falciparum 3d7 genome (asm276v1) using partek flow. all aligned files […]

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