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Protocols

PermutMatrix specifications

Information


Unique identifier OMICS_13005
Name PermutMatrix
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data Subset of gene expression data
Input format TXT, XLS, EISEN’S CLUSTER (format)
Operating system Windows
Programming languages C++
Computer skills Advanced
Version 1.9.3
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Gilles Caraux

Publication for PermutMatrix

PermutMatrix citations

 (113)
call_split

Proteomic alterations in early stage cervical cancer

2018
Oncotarget
PMCID: 5915062
PMID: 29719595
DOI: 10.18632/oncotarget.24773
call_split See protocol

[…] ealthy epithelium. The IPA classified proteins were clustered individually in samples from the groups early and late stage cervical cancer and healthy epithelium. For hierarchical clustering analysis PermutMatrix 1.9.3. was used (http://www.atgc-montpellier.fr/permutmatrix) selecting the Euclidean distance for dissimilarity, Wards’ method, as a cluster method and Bipolarization seriation [, ]. […]

library_books

GABA and GABA Alanine from the Red Microalgae Rhodosorus marinus Exhibit a Significant Neuro Soothing Activity through Inhibition of Neuro Inflammation Mediators and Positive Regulation of TRPV1 Related Skin Sensitization

2018
Mar Drugs
PMCID: 5867640
PMID: 29562624
DOI: 10.3390/md16030096

[…] ) into regular bins, i.e., chemical shift intervals of ∆δ = 0.2 ppm, and to associate the absolute intensity of each 13C NMR peak with the corresponding bin. The resulting table was imported into the PermutMatrix version 1.9.3 software (LIRMM, Montpellier, France) for clustering analysis on raw peak intensity values. The classification was performed on the rows only, i.e., on the chemical shift bi […]

library_books

Identification and characterization of microRNA in the lung tissue of pigs with different susceptibilities to PCV2 infection

2018
PMCID: 5815207
PMID: 29448950
DOI: 10.1186/s13567-018-0512-3

[…] old-change and P value of each miRNA in each sample pair were calculated using previously published criteria [–]. A hierarchical clustering analysis of the miRNA expression levels was performed using PermutMatrix software. The relative expression level of each miRNA was calculated as the total number of reads in the four libraries. […]

library_books

Nanoparticle antagomiR based targeting of miR 31 to induce osterix and osteocalcin expression in mesenchymal stem cells

2018
PLoS One
PMCID: 5812622
PMID: 29444183
DOI: 10.1371/journal.pone.0192562

[…] side and primers on the other. Afterwards the plate was run using the BioMark Fluidigm system. Data was obtained by Fluidigm Real-Time PCR Analysis Software. Heatmaps were produced using the software PermutMatrix v.1.9.3. […]

library_books

Expression analysis of candidate genes for fatty acid composition in adipose tissue and identification of regulatory regions

2018
Sci Rep
PMCID: 5794915
PMID: 29391556
DOI: 10.1038/s41598-018-20473-3

[…] kage. The remaining residuals of the phenotypes and gene expression values corrected for the corresponding effects were used to obtain the pairwise correlations. The hierarchical clustering option of PermutMatrix software was used to visualize the results of both traits and genes. […]

library_books

Insights into the molecular regulation of monolignol derived product biosynthesis in the growing hemp hypocotyl

2018
BMC Plant Biol
PMCID: 5749015
PMID: 29291729
DOI: 10.1186/s12870-017-1213-1

[…] he differentially abundant proteins was obtained using the same parameters as for 2D–DiGE (fold-change (NSAF) > 1.5 and Student’s t-test p-value below 0.05). The NSAF values have been displayed using PermutMatrix [] with the following parameters: dissimilarity assessed by Pearson distance, clustering in complete linkage, seriation and tree seriation in multiple-fragment heuristic (MF), rows normal […]


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PermutMatrix institution(s)
Laboratoire d’Informatique de Robotique et de Microélectronique de Montpellier, Montpellier, France; Ecole Nationale Supérieure Agronomique de Montpellier, Montpellier, France; Research School of Biological Sciences, Australian National University, Canberra, Australia

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