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Protocols

Explicet specifications

Information


Unique identifier OMICS_01497
Name Explicet
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Publication for Explicet

Explicet citations

 (45)
library_books

Microbiome and Culture Based Analysis of Chronic Rhinosinusitis Compared to Healthy Sinus Mucosa

2018
Front Microbiol
PMCID: 5932350
PMID: 29755418
DOI: 10.3389/fmicb.2018.00643

[…] ds, 5,927,565 reads were classified in 1,200 bacterial genera (OTUs), and for 55,966 reads had no relative sequence were found.OTU counts based on genus level rank classification were sum-normalized. Explicet (Robertson et al., ) was used for providing bootstraped-based subsampling for normalizing OTU counts in the bacterial richness analysis. For this analysis four samples with less than 19,360 r […]

library_books

BURRITO: An Interactive Multi Omic Tool for Visualizing Taxa–Function Relationships in Microbiome Data

2018
Front Microbiol
PMCID: 5837987
PMID: 29545787
DOI: 10.3389/fmicb.2018.00365

[…] r functional profiles are then often visualized as simple stacked bar or area plots of relative abundances, or via specialized data visualization tools designed for exploring these data. For example, Explicet () and Krona () aid analysis by displaying abundance data while simultaneously presenting the hierarchical relationships between entities. Other tools have gone beyond relative abundance visu […]

library_books

Benthic Bacterial Community Composition in the Oligohaline Marine Transition of Surface Sediments in the Baltic Sea Based on rRNA Analysis

2018
Front Microbiol
PMCID: 5827536
PMID: 29520255
DOI: 10.3389/fmicb.2018.00236

[…] Richness was estimated using Explicet () based on a bootstrapped rarefaction (rarefaction point at 12,833 reads). A Kruskal-Wallis test and a post hoc Tukey’s pairwise test was used to calculate significant differences between th […]

call_split

Longitudinal microbiome analysis of single donor fecal microbiota transplantation in patients with recurrent Clostridium difficile infection and/or ulcerative colitis

2018
PLoS One
PMCID: 5791968
PMID: 29385143
DOI: 10.1371/journal.pone.0190997
call_split See protocol

[…] test and chi-square analysis using GraphPAD prism.Alpha diversity indices (e.g. Chao1, Shannon complexity H, Shannon Evenness H/Hmax) were calculated inferred through 1000 replicate resamplings using Explicet [], and beta diversity (Bray-Curtis and Jaccard distances) were calculated between the recipient samples and their paired donor samples as previously described []. A linear mixed model was us […]

call_split

Pyrroloquinoline quinone prevents developmental programming of microbial dysbiosis and macrophage polarization to attenuate liver fibrosis in offspring of obese mice

2018
PMCID: 5831029
PMID: 29507905
DOI: 10.1002/hep4.1139
call_split See protocol

[…] Mann‐Whitney U test using Prism 6.0. Statistical differences were determined as significant for P < 0.05. MetaboAnalyst (www.metaboanalyst.ca) was used for display and analysis of metabolomics data. Explicet (v2.10.5) and R were used for display and analysis of microbiota data. Permutation‐based analysis of variance tests were performed using Bray‐Curtis dissimilarity scores and 100,000 replicate […]

call_split

Evaluation of bloodstream infections, Clostridium difficile infections, and gut microbiota in pediatric oncology patients

2018
PLoS One
PMCID: 5766145
PMID: 29329346
DOI: 10.1371/journal.pone.0191232
call_split See protocol

[…] All data analyses were performed using the Explicet and R statistical software packages.[, ] The relative abundance (RA) of each taxon was calculated as the number of 16S rRNA sequences of a given taxon divided by the total number of 16S rRNA […]

Citations

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Explicet institution(s)
Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA; University of Colorado Microbiome Research Consortium, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO, USA; Incubix Incorporated, Boulder, CO, USA; Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA

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