Partek Genomics Suite protocols

Partek Genomics Suite specifications

Information


Unique identifier OMICS_01133
Name Partek Genomics Suite
Software type Package/Module
Interface Command line interface
Restrictions to use License purchase required
Operating system Unix/Linux
License Commercial
Computer skills Advanced
Stability Stable
Maintained Yes

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Partek Genomics Suite IN pipelines

 (13)
2018
PMCID: 5955139
PMID: 29774125
DOI: 10.18632/oncotarget.25188

[…] expression values. transcripts with maximum global expression greater than 1 and log fold-change greater than 1.5 were selected for go analysis in enrichr [16]. heat maps were visualized with partek genomics suite 6.6 (st. louis, mo) and scatterplots were visualized with stata/mp 14.2 (college station, tx)., at least three independent experiments were performed in triplicate, and data […]

2017
PMCID: 5516996
PMID: 28723918
DOI: 10.1371/journal.pone.0180873

[…] was performed based on the gene ontology (go) and kegg (kyoto encyclopedia of genes and genomes) annotation using partek pathway. we also transferred the normalized data from partek flow into partek genomics suite to perform pathway anova using the kegg annotation database. this procedure tests for shifts in the expression of all of the transcripts represented in a particular gene set, […]

2017
PMCID: 5635513
PMID: 29017458
DOI: 10.1186/s12864-017-4151-2

[…] tmm normalization, a generalized linear model, and fdr calculations based on the benjamini-hochberg method [102]. hierarchical clustering, heatmap generation, and pca analysis were performed using partek genomics suite. go term enrichment analysis was performed using the gohypergall script [103] with a fdr cut-off of 10−3., primers (additional file 2: table s9) were designed to amplify bands […]

2017
PMCID: 5650373
PMID: 29088818
DOI: 10.18632/oncotarget.20345

[…] annotation database and the quantification of relative abundance of each transcript was reported as fragments per kilobase of transcript per million mapped reads (fpkm). anova test was conducted (on partek genomics suite) to identify mrnas with differential expression between tumors and matched normal adjacent tissues using the threshold false discovery rate (fdr) ≤ 0.05. genes with at least 2 […]

2016
PMCID: 5008286
PMID: 26802029
DOI: 10.18632/oncotarget.6965

[…] expression levels, mature mirna sequences were used to search mirna fastq files and normalized to counts per million total reads for each sample. for statistical analysis and clustering, we used the partek genomics suite software package (partek inc). fpkm (mrna) or counts per million total reads (mirna) values were log base 2 transformed and mean centered before clustering., bisulfate dna […]

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