Biome-Shiny v1.0
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Data Type
Biom file
Sample dataset
Type of biom file:
.biom file with sample variables
.biom file with .csv metadata file
.biom file without .csv metadata file
Dataset:
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OTU Table: Samples are columns
.csv metadata file (sample variables):
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Taxonomy parsing function
Default
QIIME
Greengenes
Choose a sample dataset:
dietswap
atlas1006
Update Dataset
Rarefaction
Top taxa
Subset taxa
Remove samples
Data Filtering and Transformation
Rarefy dataset
Seed
Sample with replace
Remove non-top taxa
Number of top taxa:
Subset taxa by taxonomy rank
Uncheck all taxa
Check all taxa
Taxa rank:
Taxa:
Uncheck all samples
Check all samples
Remove unchecked samples
Samples:
Activate changes
Set as active dataset
Phyloseq Summary
Sample variables:
Variables
Absolute Abundance Plot
Relative Abundance Plot
Settings
Sample variable:
Transparent background
Group samples by metadata variable (facet_wrap)
Metadata:
Taxonomy
Taxonomic rank:
Phylum
Class
Order
Family
Genus
Richness Plot
Evenness Table
Abundance Table
Richness Table
Metadata Table
Plot Settings
Plot
Variables
Samples:
Point color:
Transparent background
Sort samples by metadata variable
Sample sorting metadata:
Diversity measure:
Observed
Chao1
ACE
Shannon
Simpson
InvSimpson
Fisher
Download
Abundance (Counts)
Abundance (Relative)
Download
Download
Download
Download
Ordination Plot
Taxa Plot
Variables
Plot
Variables
Metadata:
Ordination method:
DCA
CCA
RDA
CAP
DPCoA
NMDS
MDS
PCoA
Distance:
bray
jaccard
unifrac
Aesthetic options:
Dataset: Transform data with Hellinger method
Point size:
Transparent background
Variables
Plot
Variables
Taxonomy rank:
Phylum
Class
Order
Family
Genus
Ordination method:
DCA
CCA
RDA
CAP
DPCoA
NMDS
MDS
PCoA
Distance:
bray
jaccard
unifrac
Aesthetic options:
Point size:
Enable facet_wrap
Transparent background
P-Value
Top Factors
Network Plot
Variables
Data Tables
Variables
Dissimilarity index:
manhattan
euclidean
canberra
clark
bray
kulczynski
jaccard
gower
altGower
morisita
horn
mountford
raup
binomial
chao
cao
mahalanobis
Sample variable:
Number of permutations:
P-Value table
Download
Homogeniety table
Download
Variables
Plot
Variables
Dissimilarity index:
manhattan
euclidean
canberra
clark
bray
kulczynski
jaccard
gower
altGower
morisita
horn
mountford
raup
binomial
chao
cao
mahalanobis
Sample variable:
Number of permutations:
Variables
Plot
Variables
Distance method:
bray
jaccard
unifrac
Transparent background
Sample variable to cluster data samples:
Update
Sample variable to set different point shapes:
Update
Download
HTML
Download report