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joey711
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phyloseq
phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
http://joey711.github.io/phyloseq/
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Phyloseq error issue: print(plot_ordination(GP.ord_ITS, color = "Treatment", label = "Sample_ID", title = "ITS Combined") + geom_point(size = 3) + geom_text(size = 5, vjust = 1.5)) #Error message: Warning: Full functionality requires `physeq` be phyloseq-class with multiple components.Warning: Could not obtain coordinates from the provided `ordination`.
#1726
cortez10arizona
opened
9 months ago
0
Rename ASVs in otu_table as sub-types
#1725
AngelicaMiraples
opened
9 months ago
3
Hi @marwa38 You can do this without using functions from the `microbiome` package.
#1724
ElizabethOLeary
closed
9 months ago
0
duplicate ‘row.names’ are not allowed
#1723
bdonnelly112493
opened
9 months ago
0
How to filter out ASVs on a per-sample basis, based on some relative abundance threshold?
#1722
J-W-Romero
opened
10 months ago
0
object '.graphStack' not found
#1721
slambrechts
opened
10 months ago
0
Is it possible to add two taxa.label to heatmaps?
#1720
we32i225
opened
10 months ago
0
Using phyloseq for metagenomic data without actual OTUs
#1719
CETHuyghe
opened
10 months ago
0
merge_phyloseq with phy_tree containing different number of tips
#1718
AngelicaMiraples
closed
10 months ago
0
Biplot with plot_ordination using PCoA and Bray distance
#1717
microtonio
opened
10 months ago
0
phyloseq_filter_prevalence, non-zero dimension
#1716
JH966
opened
11 months ago
0
Summary of the Advisory Opinion of 16 October 1975 | INTERNATIONAL COURT OF JUSTICE
#1715
Ambassadormathismathews
opened
11 months ago
0
customize facet colors in ggplot/ phyloseq object
#1714
science-chump
opened
12 months ago
1
How to merge the same data for analysis?
#1713
lingvv
opened
12 months ago
1
Thanks Michelle, it makes sense now. I'll keep that in mind next time I label.
#1712
Ambassadormathismathews
opened
1 year ago
1
filter_taxa after tax_glom
#1711
chrissy005
opened
1 year ago
0
Import qiime2 table.qza error-reg
#1710
Balakulandai
opened
1 year ago
0
duplicate sample with different variable value
#1709
francescaangiol
opened
1 year ago
0
estimate_richness fails -- Component taxa/OTU names do not match.
#1708
r-mashoodh
opened
1 year ago
2
New feature: allow merge_taxa to keep recored of merged (and inextension tax_glom).
#1707
derele
opened
1 year ago
0
Give same ASV names between 3 datasets
#1706
pailloufat-stack
opened
1 year ago
0
Tax_glom error after transform_sample_counts
#1705
DanieleDeco
opened
1 year ago
0
tax_glom, invalid archetype provided
#1704
Thyreus
opened
1 year ago
1
Software Compatibility Issue Between phyloseq and lme4 Packages
#1703
FrederickHuangLin
opened
1 year ago
4
Filtering reads and OUTs of low abundance
#1702
HNihad
opened
1 year ago
0
How I can plot relative abundance by sampling site instead of by sample ID?
#1701
Ecotone23
opened
1 year ago
9
How to tabulate most abundant ASVs by treatment
#1700
J-W-Romero
opened
1 year ago
0
common otus with low coefficient of variation that are observed in at least once in more than 2 sites
#1699
beatencio
opened
1 year ago
0
How to mask seriation Complex heat map
#1698
plaw1985
closed
1 year ago
2
invalid archetype error for tax_glom
#1697
hkittner
opened
1 year ago
0
how to replace "unidentified" taxa as NA in phyloseq object
#1696
plaw1985
closed
1 year ago
2
Scoping issues in subset_taxa (and probably other similar functions)
#1695
mhoban
opened
1 year ago
1
Error in eigen(delta1) : error code 1 from Lapack routine 'dsyevr'
#1694
Gian77
opened
1 year ago
2
What is the difference between prune_samples, rarefy and rarefy_even_depth functions?
#1693
Ecotone23
opened
1 year ago
2
import_biom: HDF5 format warnings
#1692
biobee
opened
1 year ago
3
Help with error: invalid class “phyloseq” object: component sample names do not match
#1691
Ecotone23
closed
1 year ago
3
can I add a condition to merge_samples?
#1690
lauraDRH
opened
1 year ago
2
Doubled abundance value after tax_glom
#1689
bennend
opened
1 year ago
1
Sudden Error with the distance() function
#1688
Aliceall
closed
1 year ago
2
Normalization for alpha diversity analyses
#1687
otaviolovison
opened
1 year ago
2
plot_ordination function plots shapes 'double' within itself
#1686
Robvh-git
closed
1 year ago
2
Calculating weighted Unifrac Distance from CLR Data
#1685
JLammons14
opened
1 year ago
2
ps_filter not an available function
#1684
KaraS106
opened
1 year ago
2
issues importing data- sp1, sp2 etc column added to taxonomy table
#1683
KaraS106
opened
1 year ago
1
R studio graph plot, samples are not together
#1682
Hina1112
opened
1 year ago
2
missing reads after phyloseq() step
#1681
Rosiekstein
opened
1 year ago
1
ASV reduction/pruning in phyloseq object
#1680
camcecc
opened
1 year ago
1
I count not arrange my sample from same group together
#1679
Hina1112
opened
1 year ago
3
trouble with using the output from idtaxa with phyloseq
#1678
MCK-sketch
opened
1 year ago
1
problem loading phyloseq
#1677
sclknowles
opened
1 year ago
1
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