Partek Flow statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Partek Flow
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Tool usage distribution map

This map represents all the scientific publications referring to Partek Flow per scientific context
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Associated diseases

This word cloud represents Partek Flow usage per disease context
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Popular tool citations

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

Partek Flow specifications

Information


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

Versioning


No version available

Additional information


A free trial is available on the site.

Partek Flow citations

 (48)
call_split

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

2018
PLoS One
PMCID: 5918994
PMID: 29694377
DOI: 10.1371/journal.pone.0196058
call_split See protocol

[…] because the corresponding website is no longer functioning.The datasets from [] come in BAM format (aligned with BWA), whereas TrueSeq datasets are downloaded in FASTQ format and aligned with BWA in Partek Flow. After that, duplicates are removed using Filter Alignments task and the variant calls are obtained using Samtools and Freebayes in Partek Flow. For WES data, the calls are restricted to t […]

call_split

The striatal kinase DCLK3 produces neuroprotection against mutant huntingtin

2018
PMCID: 5917821
PMID: 29534157
DOI: 10.1093/brain/awy057
call_split See protocol

[…] v2 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 (the […]

call_split

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

2018
Sci Rep
PMCID: 5838106
PMID: 29507358
DOI: 10.1038/s41598-018-22409-3
call_split See protocol

[…] xt-generation 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 On […]

call_split

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

2017
PMCID: 5750478
PMID: 29244788
DOI: 10.1038/emm.2017.226
call_split See protocol

[…] 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 […]

call_split

Hippocampal Transcriptomic Profiles: Subfield Vulnerability to Age and Cognitive Impairment

2017
PMCID: 5727020
PMID: 29276487
DOI: 10.3389/fnagi.2017.00383
call_split See protocol

[…] s resulting in reads containing an average length of 134 bp. The Ion Proton data were aligned to the rattus norvegicus (rn5) genome using the two step alignment method with TopHat2 and Bowtie2 in the Partek Flow servers (Partek, Inc.). Aligned reads were summarized as gene-level counts (featureCounts 1.4.4). The FASTQ files from the Ion Proton have been submitted to NCBI's Gene Expression Omnibus […]

library_books

Malaria parasite DNA harbouring vesicles activate cytosolic immune sensors

2017
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 wer […]


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