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ampvis specifications

Information


Unique identifier OMICS_28643
Name ampvis
Alternative name ampvis2
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 2.3.3
Stability Stable
Maintained Yes

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Versioning


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Documentation


Maintainer


  • person_outline Mads Albertsen

Publications for ampvis

ampvis citations

 (17)
library_books

The biogeochemical vertical structure renders a meromictic volcanic lake a trap for geogenic CO2 (Lake Averno, Italy)

2018
PLoS One
PMCID: 5839588
PMID: 29509779
DOI: 10.1371/journal.pone.0193914

[…] NGS results were analyzed in R (R Core Team 2015) through the Rstudio IDE using the ampvis package v.1.9.1 []. Data in the OTU table were normalized to percent. Moreover, in order to calculate to calculate alpha-diversity the data were normalized to the same number of reads (subsampl […]

call_split

Diversity and metabolic potential of the microbiota associated with a soil arthropod

2018
Sci Rep
PMCID: 5802828
PMID: 29410494
DOI: 10.1038/s41598-018-20967-0
call_split See protocol

[…] g SILVA (version 128) as the reference database.The statistical analyses and visualizations were performed in R version 3.3.3 via RStudio version 1.0.143 (http://www.rstudio.com) using the R packages ampvis and phyloseq. Biodiversity was explored through the observed number of OTUs and diversity indices ChaoI, and Shannon-Weaver,. Diversity indices did not meet the assumptions of equal variances, […]

library_books

Microbes and associated soluble and volatile chemicals on periodically wet household surfaces

2017
Microbiome
PMCID: 5615633
PMID: 28950891
DOI: 10.1186/s40168-017-0347-6

[…] TU identified as Amanita phalloides likely resulting from barcode bleed [] with other samples sequenced in the same MiSeq library.The OTU tables were analyzed in R [] using the vegan [], Phyloseq [], ampvis [], and ggplot2 [] packages, which created the functionality to graphically summarize the data as heatmaps, constrained ordination, and relative abundance barplots.Quantitative PCR was done on […]

library_books

The ClpXP protease is dispensable for degradation of unfolded proteins in Staphylococcus aureus

2017
Sci Rep
PMCID: 5603545
PMID: 28924169
DOI: 10.1038/s41598-017-12122-y

[…] ssed using the default DESeq. 2 workflow and visualized using ggplot2. PCA analysis of overall sample similarity was done using DESeq. 2 normalized counts (square root transformed), through the vegan ampvis R packages. […]

library_books

Comparison of the bacterial community composition in the granular and the suspended phase of sequencing batch reactors

2017
PMCID: 5583138
PMID: 28871435
DOI: 10.1186/s13568-017-0471-5

[…] cies richness and Pielou’s evenness were calculated using the package vegan (Oksanen et al. ), non-metric multi-dimensional scaling (NMDS) ordination plots and heatmaps were created using the package ampvis (Albertsen et al. ), and basic R functions were used to create the Tukey boxplots, perform one-sample Wilcoxon signed-rank tests and calculate Pearson correlation coefficients (r). The sequence […]

call_split

The impact of immigration on microbial community composition in full scale anaerobic digesters

2017
Sci Rep
PMCID: 5571154
PMID: 28839166
DOI: 10.1038/s41598-017-09303-0
call_split See protocol

[…] Further processing of the OTU table was carried out in the R environment (v. 3.3.2) using the R studio IDE using the ampvis package (v. 1.27.0) for visualisation. The ampvis package wraps a number of packages including the phyloseq package (v. 1.19.1), ggplot2 (v. 2.2.1), reshape2 (v. 1.4.2), dplyr (v. 0.5.0), vegan […]

Citations

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ampvis institution(s)
Center for Microbial Communities, Aalborg University, Aalborg, Denmark
ampvis funding source(s)
Supported by a research grant (15510) from VILLUM FONDEN.

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