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EMPeror specifications

Information


Unique identifier OMICS_07236
Name EMPeror
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Requirements
Numpy, SciKit-bio, qcli
Maintained Yes

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Publication for EMPeror

EMPeror citations

 (100)
library_books

American Gut: an Open Platform for Citizen Science Microbiome Research

2018
mSystems
PMCID: 5954204
DOI: 10.1128/mSystems.00031-18

[…] ad length in the work of Yatsunenko et al. (). Bloom reads as described above were removed from all samples. We used Striped UniFrac as noted above to estimate beta-diversity (unweighted UniFrac) and EMPeror software () version 0.9 to visualize principal coordinates. We used a nonparametric PERMANOVA with 999 permutations to test for significant differences in fecal microbiomes associated with ind […]

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Lactobacilli Are Prominent Members of the Microbiota Involved in the Ruminal Digestion of Barley and Corn

2018
Front Microbiol
PMCID: 5902705
PMID: 29692773
DOI: 10.3389/fmicb.2018.00718
call_split See protocol

[…] ersity) within biofilms from all four barley varieties and corn was evaluated using the unweighted and weighted UniFrac distances () and visualized as principal coordinate analysis (PCoA) plots using Emperor (). ANOSIM (analysis of similarities) with 999 permutations was used to compare the unweighted UniFrac distances.Linear discriminant analysis effect size (LefSe) was used to determine which ta […]

library_books

Response of Aquatic Bacterial Communities to Hydraulic Fracturing in Northwestern Pennsylvania: A Five Year Study

2018
Sci Rep
PMCID: 5890257
PMID: 29632304
DOI: 10.1038/s41598-018-23679-7

[…] ed OTU table was used to perform beta diversity analysis. Beta diversity was calculated using the weighted Unifrac distance metric and principal coordinate analysis (PCoA) plots were visualized using EMPeror. Mean Unifrac distances were calculated between sample clusters were reported. Adonis tests were performed on the weighted Unifrac values to determine the variation explained by stream water c […]

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Increased gut permeability in cancer cachexia: mechanisms and clinical relevance

2018
Oncotarget
PMCID: 5915068
PMID: 29719601
DOI: 10.18632/oncotarget.24804
call_split See protocol

[…] proportions based on the total number of sequences in each sample. Beta-diversity indexes and Adonis values were calculated using QIIME []. PCoA plot of the beta-diversity indexes were obtained using EMPeror []. The LDA effect size was computed and plotted using LEfSe []. Sequences can be found in the MG-RAST database (projects ID Cachexia_1, Cachexia_pair_feeding, Cachexia_IL6). […]

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Variation in the microbiome of the urogenital tract of Chlamydia free female koalas (Phascolarctos cinereus) with and without ‘wet bottom’

2018
PLoS One
PMCID: 5868818
PMID: 29579080
DOI: 10.1371/journal.pone.0194881
call_split See protocol

[…] ost influential principal coordinates were drawn from the resulting distance matrices either using either the make_2d_plots.py QIIME script, or within the beta_diversity_through_plots.py script using EMPeror 9.51 software [], respectively. Distance and dissimilarity metrics were used to compare the microbial communities between the two groups by utilising the permutational ANOVA (PERMANOVA) [] met […]

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Evaluation of milk sample fractions for characterization of milk microbiota from healthy and clinical mastitis cows

2018
PLoS One
PMCID: 5862444
PMID: 29561873
DOI: 10.1371/journal.pone.0193671
call_split See protocol

[…] coordinates were computed from the calculated UniFrac distance matrix to compress dimensionality into three-dimensional principal coordinate analysis (PCoA) plots created by QIIME 2 and visualized by EMPeror []. Differences between microbial communities (beta diversity) based on phylogenetic information visualized on the PCoA plots were calculated by permutational multivariate analysis of variance […]

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EMPeror institution(s)
BioFrontiers Institute, University of Colorado at Boulder, Boulder, CO, USA

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