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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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Merging sequencing runs containing different studies using merge_phyloseq?
#1763
punnettsun
opened
1 week ago
0
Taxa names coming up as random words
#1762
backwards-charm
opened
1 week ago
7
technical question using ordinate phyloseq function with envfit of vegan Package
#1761
cabraham03
opened
1 week ago
0
Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘tax_table’ for signature ‘"list"or"matrix"
#1760
npj06
opened
1 week ago
0
webR support
#1759
isbool
opened
2 weeks ago
0
plot_tree and taxonomy
#1758
antoine4ucsd
opened
3 weeks ago
0
Abundance Plot Help
#1757
goodguynickpt
opened
3 weeks ago
0
Heatmap color fade
#1756
goodguynickpt
opened
3 weeks ago
0
Subtracting taxa from a phyloseq object
#1755
GinaGizzi
opened
1 month ago
0
Taxa abundance with plot_bar - Can the color squares in the key be reduced in size?
#1754
atozga
opened
1 month ago
0
rarefy_even_depth() Error en rep_len(x["OTUi"], x["times"]): valor de 'length.out' no válido
#1753
imonteroo
opened
1 month ago
0
Error : invalid class “phyloseq” object: Component taxa/OTU names do not match.
#1752
Saesha5
opened
1 month ago
0
Plot_Networt by Phyloseq Object
#1751
Motteran
opened
1 month ago
0
Remove mitochondrial and chloroplastic taxons from my phyloseq object
#1750
pailloufat-stack
opened
1 month ago
0
Error when using hellinger transformation with ordinate and PCoA
#1749
timz0605
opened
2 months ago
0
plot_tree: Added ggplot code to fix ugly legend "a"s
#1748
stephanbitterwolf
opened
2 months ago
0
Extremely wide variation of alpha diversity estimates among different studies
#1747
migfejo
opened
2 months ago
0
Missing reads creating phyloseq object after dada2 pipeline
#1746
GingerMATE
opened
2 months ago
1
Run the Wilcoxon test for each of the taxa ranks
#1745
mailasb
opened
2 months ago
0
`merge_phyloseq` fails if sample data contains only one column
#1744
ying14
opened
2 months ago
2
Is it possible to transform sample counts by value stored in sample data?
#1743
tacaro
closed
2 months ago
1
Failure to merge files into a phyloseq object after renaming taxa, and sequences
#1742
emankhalaf
closed
2 months ago
2
Creating a relative abundance bar plot by body site
#1741
bark9299
opened
2 months ago
0
MicroViz error Error in (function (cond) : error in evaluating the argument 'object' in selecting a method for function 'otu_table': Can't find column `OTU_ID` in `.data`.
#1740
Jesuk555
opened
3 months ago
1
Difference in relative abundance between MicrobiomeDB and r phyloseq
#1739
kbenmd
opened
3 months ago
0
How to decrease x axis size of rarefaction curve
#1738
Avtober
opened
3 months ago
1
Very High Log2FoldChanges
#1737
TamarSmulders
opened
3 months ago
2
Error in eval(call("force", as.symbol(paste0("..", x))))
#1736
fconstancias
closed
3 months ago
3
Facet Taxa axis in Phyloseq heatmap
#1735
jrb772
opened
3 months ago
0
merging two phyloseq objects is duplicating phyloseq objects
#1734
lauraDRH
opened
4 months ago
0
Phyloseq taxa don't match error, but TRUE when asked if values match?
#1733
hank00000
opened
4 months ago
4
Showing top 5 genus in ordination plot legend
#1732
Arrowessee
closed
3 months ago
3
Reverse the color of legend in phyloseq tree plot
#1731
Arrowessee
opened
4 months ago
0
.
#1730
Arrowessee
closed
3 months ago
1
reorganization of x-axis for heat plot, using factors as x-axis
#1729
science-chump
opened
4 months ago
0
phyloseq x metagMisc phyloseq_coverage_raref: Error "OTU abundance data must have non-zero dimensions"
#1728
PeSteff
opened
4 months ago
0
Diff Normalization Method- Upload Back Into Phyloseq Format?
#1727
hank00000
closed
4 months ago
1
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
4 months ago
0
Rename ASVs in otu_table as sub-types
#1725
AngelicaMiraples
opened
4 months ago
3
Hi @marwa38 You can do this without using functions from the `microbiome` package.
#1724
ElizabethOLeary
closed
5 months ago
0
duplicate ‘row.names’ are not allowed
#1723
bdonnelly112493
opened
5 months ago
0
How to filter out ASVs on a per-sample basis, based on some relative abundance threshold?
#1722
J-W-Romero
opened
5 months ago
0
object '.graphStack' not found
#1721
slambrechts
opened
5 months ago
0
Is it possible to add two taxa.label to heatmaps?
#1720
we32i225
opened
5 months ago
0
Using phyloseq for metagenomic data without actual OTUs
#1719
CETHuyghe
opened
5 months ago
0
merge_phyloseq with phy_tree containing different number of tips
#1718
AngelicaMiraples
closed
5 months ago
0
Biplot with plot_ordination using PCoA and Bray distance
#1717
microtonio
opened
5 months ago
0
phyloseq_filter_prevalence, non-zero dimension
#1716
JH966
opened
6 months ago
0
Summary of the Advisory Opinion of 16 October 1975 | INTERNATIONAL COURT OF JUSTICE
#1715
Ambassadormathismathews
opened
7 months ago
0
customize facet colors in ggplot/ phyloseq object
#1714
science-chump
opened
7 months ago
1
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