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/

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issues

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Mock Communities - Observed vs Expected

#1776 andrebolerbarros opened 4 days ago
1
import_biom issue

#1775 skose82 opened 3 weeks ago
0
Phyloseq package citation

#1774 UniAlberta opened 1 month ago
2
Error in access(object, "otu_table", errorIfNULL) :

#1773 kdbchau opened 1 month ago
0
Where to find CAP1 and CAP2 values in phyloseq::ordinate with method "CAP"

#1772 msconstante opened 2 months ago
1
merge_phyloseq deleting samples

#1771 efgellerson opened 2 months ago
1
Strange issue when importing data

#1770 msuokas-bco opened 2 months ago
0
pruning taxa using sequence lengths (width)

#1769 sghignone closed 2 months ago
1
Error: unable to find an inherited method for function ‘normalize’ for signature ‘object = "phyloseq"’

#1768 Saeedjaanz opened 3 months ago
0
Weighted and Unweighted PCoA have the exact same values

#1767 goodguynickpt closed 3 months ago
0
sorry, delete this issue I had made an error

#1766 arthurltaylor opened 3 months ago
0
How to add scale bar in tree

#1765 Dee-91 opened 4 months ago
0
Clashing transpose method with Matrix

#1764 BertvanderVeen opened 4 months ago
0
Merging sequencing runs containing different studies using merge_phyloseq?

#1763 punnettsun opened 4 months ago
0
Taxa names coming up as random words

#1762 backwards-charm opened 5 months ago
7
technical question using ordinate phyloseq function with envfit of vegan Package

#1761 cabraham03 opened 5 months 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 5 months ago
0
webR support

#1759 isbool opened 5 months ago
0
plot_tree and taxonomy

#1758 antoine4ucsd opened 5 months ago
0
Abundance Plot Help

#1757 goodguynickpt closed 3 months ago
0
Heatmap color fade

#1756 goodguynickpt closed 3 months ago
0
Subtracting taxa from a phyloseq object

#1755 GinaGizzi opened 6 months ago
0
Taxa abundance with plot_bar - Can the color squares in the key be reduced in size?

#1754 atozga opened 6 months ago
0
rarefy_even_depth() Error en rep_len(x["OTUi"], x["times"]): valor de 'length.out' no válido

#1753 imonteroo opened 6 months ago
0
Error : invalid class “phyloseq” object: Component taxa/OTU names do not match.

#1752 Saesha5 opened 6 months ago
0
Plot_Networt by Phyloseq Object

#1751 Motteran opened 6 months ago
0
Remove mitochondrial and chloroplastic taxons from my phyloseq object

#1750 pailloufat-stack opened 6 months ago
0
Error when using hellinger transformation with ordinate and PCoA

#1749 timz0605 opened 6 months ago
1
plot_tree: Added ggplot code to fix ugly legend "a"s

#1748 stephanbitterwolf opened 7 months ago
0
Extremely wide variation of alpha diversity estimates among different studies

#1747 migfejo opened 7 months ago
0
Missing reads creating phyloseq object after dada2 pipeline

#1746 GingerMATE opened 7 months ago
1
Run the Wilcoxon test for each of the taxa ranks

#1745 mailasb opened 7 months ago
0
`merge_phyloseq` fails if sample data contains only one column

#1744 ying14 opened 7 months ago
2
Is it possible to transform sample counts by value stored in sample data?

#1743 tacaro closed 7 months ago
1
Failure to merge files into a phyloseq object after renaming taxa, and sequences

#1742 emankhalaf closed 7 months ago
2
Creating a relative abundance bar plot by body site

#1741 bark9299 opened 7 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 8 months ago
1
Difference in relative abundance between MicrobiomeDB and r phyloseq

#1739 kbenmd opened 8 months ago
0
How to decrease x axis size of rarefaction curve

#1738 Avtober opened 8 months ago
1
Very High Log2FoldChanges

#1737 TamarSmulders opened 8 months ago
2
Error in eval(call("force", as.symbol(paste0("..", x))))

#1736 fconstancias closed 8 months ago
3
Facet Taxa axis in Phyloseq heatmap

#1735 jrb772 opened 8 months ago
0
merging two phyloseq objects is duplicating phyloseq objects

#1734 lauraDRH opened 8 months ago
0
Phyloseq taxa don't match error, but TRUE when asked if values match?

#1733 hank00000 opened 9 months ago
4
Showing top 5 genus in ordination plot legend

#1732 Arrowessee closed 8 months ago
3
Reverse the color of legend in phyloseq tree plot

#1731 Arrowessee opened 9 months ago
0
.

#1730 Arrowessee closed 8 months ago
1
reorganization of x-axis for heat plot, using factors as x-axis

#1729 science-chump opened 9 months ago
0
phyloseq x metagMisc phyloseq_coverage_raref: Error "OTU abundance data must have non-zero dimensions"

#1728 PeSteff opened 9 months ago
0
Diff Normalization Method- Upload Back Into Phyloseq Format?

#1727 hank00000 closed 9 months ago
1