joey711 phyloseq issues

joey711 / 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/

567 stars 187 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Merging sequencing runs containing different studies using merge_phyloseq?

#1763 punnettsun opened 3 days ago
0
Taxa names coming up as random words

#1762 backwards-charm opened 6 days ago
7
technical question using ordinate phyloseq function with envfit of vegan Package

#1761 cabraham03 opened 6 days 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 6 days ago
0
webR support

#1759 isbool opened 1 week ago
0
plot_tree and taxonomy

#1758 antoine4ucsd opened 2 weeks ago
0
Abundance Plot Help

#1757 goodguynickpt opened 2 weeks ago
0
Heatmap color fade

#1756 goodguynickpt opened 2 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 1 month 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 3 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 4 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 6 months ago
0
customize facet colors in ggplot/ phyloseq object

#1714 science-chump opened 7 months ago
1