ZymoExamplePseq: ZymoExamplePseq
In microsud/chkMocks: Compare Mock Community Samples in Microbiome Sequencing Studies
ZymoExamplePseq R Documentation
ZymoExamplePseq
Description
Contains ZymoBIOMICS Microbial Community Standard samples ran
in different sequencing libraries as postive controls.
Usage
data(ZymoExamplePseq)
Format
Phyloseq object
Details
ZymoExamplePseq contains the experimental 16S composition of
ZymoBIOMICS Microbial Community Standard. 9 samples, 946 ASVs and 7
taxonomic ranks. ZymoBIOMIC mock community standards consisting of
eight bacterial species Pseudomonas.aeruginosa,
Escherichia coli, Salmonella.enterica,
Lactobacillus.fermentum, Enterococcus.faecalis,
Staphylococcus.aureus, Listeria.monocytogenes,
Bacillus.subtilis and two fungal species
Saccharomyces.cerevisiae and Cryptococcus.neoformans.
The dilutions were done in microbial free water (Qiagen) in
eight rounds of a serial three-fold dilution
prior to DNA extraction. The data are for the V4 region of the
16S rRNA gene profiled with Illumina MiSeq.
Value
Loads the data set in R.
Author(s)
Sudarshan Shetty sudarshanshetty9@gmail.com
References
Karstens L, Asquith M, Davin S, Fair D, Gregory WT, Wolfe AJ,
Braun J, McWeeney S. (2019) Controlling for contaminants in
low-biomass 16S rRNA gene sequencing experiments.
mSystems, 4:e00290-19.
https://doi.org/10.1128/mSystems.00290-19
Shetty SA 2021
microsud/chkMocks documentation built on July 1, 2023, 9:23 p.m.
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| ZymoExamplePseq | R Documentation |
ZymoExamplePseq
Description
Contains ZymoBIOMICS Microbial Community Standard samples ran in different sequencing libraries as postive controls.
Usage
data(ZymoExamplePseq)
Format
Phyloseq object
Details
ZymoExamplePseq contains the experimental 16S composition of ZymoBIOMICS Microbial Community Standard. 9 samples, 946 ASVs and 7 taxonomic ranks. ZymoBIOMIC mock community standards consisting of eight bacterial species Pseudomonas.aeruginosa, Escherichia coli, Salmonella.enterica, Lactobacillus.fermentum, Enterococcus.faecalis, Staphylococcus.aureus, Listeria.monocytogenes, Bacillus.subtilis and two fungal species Saccharomyces.cerevisiae and Cryptococcus.neoformans. The dilutions were done in microbial free water (Qiagen) in eight rounds of a serial three-fold dilution prior to DNA extraction. The data are for the V4 region of the 16S rRNA gene profiled with Illumina MiSeq.
Value
Loads the data set in R.
Author(s)
Sudarshan Shetty sudarshanshetty9@gmail.com
References
Karstens L, Asquith M, Davin S, Fair D, Gregory WT, Wolfe AJ, Braun J, McWeeney S. (2019) Controlling for contaminants in low-biomass 16S rRNA gene sequencing experiments. mSystems, 4:e00290-19. https://doi.org/10.1128/mSystems.00290-19
Shetty SA 2021
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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