JMP Genomics specifications

Information


Unique identifier OMICS_01129
Name JMP Genomics
Software type Toolkit/Suite
Interface Graphical user interface
Restrictions to use License purchase required
Operating system Unix/Linux, Windows
Computer skills Medium
Version 13.2.1
Stability Stable
Free trial Yes
Maintained Yes

Versioning


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Documentation


Maintainer


  • person_outline JMP Genomics Team <>

Additional information


https://www.jmp.com/en_us/support/jmp-documentation.html

JMP Genomics citations

 (6)
2017
PMCID: 5387399

[…] count files from the rnaseq reads, the data were primarily filtered to remove transcripts with low counts (sum of counts less than 100 across samples). filtered samples were kdmm normalized using jmp genomics 7.0 (sas, cary nc) and further filtered by removing rows with 40% zero counts. however, kdmm normalization could not normalize the outliers present in the experiment. so, to avoid bias […]

2015
PMCID: 4415818

[…] hybridization, scanning, data normalization and assessment of statistically and biologically significant genes were performed as described previously [37]. statistical analyses were performed using jmp genomics version 3.2 (sas institute inc., cary, nc, usa) to identify significant degs (fold change > 2) in fibers of each cotton nil at each time point with p-value ≤ 0.05. primary annotation […]

2014
PMCID: 4203797

[…] of ≥1.5 and a p value of ≤0.01. two-way hierarchical clustering, by means of ward’s minimum variance criterion method, was applied to normalized and standardized expression data using the tools in jmp genomics, version 10 (sas institute inc., cary, nc). the sage-seq analyses reported here have been deposited to geo (http://ncbi.nlm.nih.gov/geo/; accession number gse60756)., biological process […]

2014
PMCID: 4172843

[…] and samples from three independent experiments for every treatment. in each experiment, rna from cells of three filter inserts was pooled., fold changes of microarray data were calculated with the jmp genomics from sas software based on a mixed model anova. genes were regarded significantly up-regulated if differences in lg2 fold values ≥0.585 (=fold change ≥1.5) and down-regulated if lg2 fold […]

2012
PMCID: 3432130

[…] pair-wise sample correlations, pearson product-moment correlations and 2-way hierarchical clustering were all performed using jmp genomics version 4.1 (sas institute, cary, nc). we also used jmp genomics to analyze the distribution of read frequencies along the genome and also to determine statistically significant differences in fold changes between libraries., candidate genes […]

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