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Protocols

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
License Commercial
Computer skills Medium
Version 13.2.1
Stability Stable
Free trial Yes
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline JMP Genomics Team <>

Additional information


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

JMP Genomics citations

 (278)
call_split

Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose utilizing derivatives 8b and 2032

2018
PMCID: 5930841
PMID: 29743953
DOI: 10.1186/s13068-018-1116-x
call_split See protocol

[…] the reads were trimmed for nucleotides with quality score less than 30 before rna-seq analysis to get the rpkm values of protein-coding genes and rrna genes. the rpkm values were then imported into jmp genomics (https://www.jmp.com/en_us/home.html) and log2-transformed before statistical analysis similar to microarray-based transcriptomic analysis was performed [, , ]., for data normalization […]

library_books

FOXF1 Inhibits Pulmonary Fibrosis by Preventing CDH2 CDH11 Cadherin Switch in Myofibroblasts

2018
PMCID: 5947867
PMID: 29642003
DOI: 10.1016/j.celrep.2018.03.067

[…] suite (). the statistical significance of each bioprocess was calculated using a negative logarithm (−log10) of the p value. the heatmap was constructed on differentially expressed genes using jmp genomics 6.0., nih 3t3 and normal human lung fibroblast ccl-210 (atcc) cells were cultured as described previously (). plasmid and small interfering rna (sirna) transfections were performed using […]

library_books

Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics

2018
PMCID: 5887222
PMID: 29632556
DOI: 10.1186/s13068-018-1095-y

[…] very-sensitive preset option expect the number of mismatches was set to 1 [, ], and reads were counted with htseq []. principle component analysis (pca) was used to check for sample variation using jmp genomics 8 (sas institute, cary, nc, usa). differential expression analysis was performed with deseq 2 []. genes were considered significantly differential expressed when their adjusted p values […]

library_books

Revisiting the putative role of heme as a trigger of inflammation

2018
PMCID: 5878102
PMID: 29610666
DOI: 10.1002/prp2.392

[…] agilent technologies). array slides were xdr‐scanned and analyzed with feature extraction software version 10.7.3.1 (agilent technologies). statistical analysis and visualization was performed with jmp genomics 7.0 (sas institute, boeblingen, germany). full gene array data were submitted to the gene expression omnibus., reverse transcription was performed with taqman reverse transcription […]

library_books

Relation of Insulin Resistance to Longitudinal Changes in Left Ventricular Structure and Function in a General Population

2018
PMCID: 5907600
PMID: 29574459
DOI: 10.1161/JAHA.117.008315

[…] coefficients without definition of an arbitrary reference group., next, we constructed a partial regression diagram including multivariable‐adjusted changes in lv phenotype and serum insulin using jmp genomics 6.0. this approach fits covariance selection models, estimating the correlation between pairs of variables adjusted for their correlations with all other variables in the network (ie, […]

library_books

Lowered dietary phosphorus affects intestinal and renal gene expression to maintain mineral homeostasis with immunomodulatory implications in weaned piglets

2018
PMCID: 5859397
PMID: 29554878
DOI: 10.1186/s12864-018-4584-2

[…] ; 2.5) using r version 3.2.0 []. transcriptional effects were analyzed between samples from animals fed l, m, and h diets. relative changes of transcript abundance were analyzed using a linear model (jmp genomics 7.0), including the effects of diet, sire, sex, tissue, and interactions (vijkl = μ + dieti + sirej + sexk + tissuel + dieti*tissuel + errorijkl). p-values were converted to a set of q-va […]


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