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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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Need help in reordering samples for ggplot
#1676
science-chump
closed
1 year ago
2
When using phyloseq_merge, get Error in access(object, "sam_data", errorIfNULL) : sam_data slot is empty.
#1675
icbarron
opened
1 year ago
0
Error loading biom file
#1674
ana2277
opened
1 year ago
0
pca with meta data
#1673
judixy
opened
1 year ago
0
Removing phy_tree from phyloseq object
#1672
Marcelara
opened
1 year ago
1
Error "taxa_names<-: You are attempting to assign duplicated taxa_names" when substituting OTUs to Genus
#1671
francescaangiol
closed
1 year ago
2
decontam via phyloseq
#1670
judixy
closed
1 year ago
0
Is it possible to label taxa (example: degraders and non-degraders) and then plot abundance?
#1669
flsaravia
opened
1 year ago
1
How to get the explained variance form ordinate
#1668
theo-allnutt-bioinformatics
opened
1 year ago
3
tax_glom bad_empty agglomerating taxa based on NAs
#1667
jsogin574
opened
1 year ago
2
otu_table not only numeric? Estimate_richness /plot_richness doesnt work - how to troubleshoot?
#1666
mariamaseng
opened
1 year ago
1
Error in plot_net and plot_network functions
#1665
cpavloud
opened
1 year ago
0
Issues merging phyloseq files- samples names do not match
#1664
lizzy0115
closed
1 year ago
0
merge_taxa does not behave properly
#1663
ETaSky
opened
1 year ago
1
installation problem with R Studio v 4.2.2
#1662
midwesternmouse
closed
1 year ago
1
why I might be getting top 15 genus different from RA above certain threshold?
#1661
marwa38
opened
1 year ago
2
Issue creating phyloseq object
#1660
moriahy
closed
1 year ago
0
subset_taxa in loop
#1659
jeremysutherland
opened
1 year ago
1
Estimate_richness for all phyla
#1658
R-novice
opened
1 year ago
0
how to find ASVs present in different "sites"
#1657
callmcgovern
opened
1 year ago
9
Aggregate_taxa
#1656
mariamaseng
opened
1 year ago
2
Help !! plot_heatmap in R (Phyloseq) weird error
#1655
LeeJH5120
opened
1 year ago
3
How to replace the deprecated ggplot2 function aes_string?
#1654
ricmedveterinario
closed
1 year ago
4
parallelizing script for R cluster-Error- Function cannot find "tax_glom"
#1653
pulidofabs
opened
1 year ago
0
I can't get the coefficients of the taxa that contribute to the groups differences!
#1652
Srvcl
opened
1 year ago
0
Differences in number of taxa after subset_samples and prune_taxa
#1651
Alonso-Garcia
opened
1 year ago
0
rm.na.phyloseq in plot_ordination
#1650
fanhuan
closed
1 year ago
1
Difference between vegan::capscale and ordinate::(method = "CAP")?
#1649
carmennns2
opened
1 year ago
0
subset_taxa doesn't extract the taxa of my interest
#1648
mghotbi
opened
1 year ago
0
Trying to merge_phyloseq but problem with trees
#1647
xaalii
opened
1 year ago
1
loop for multiple Phyloseq object.
#1646
shashank-KU
closed
1 year ago
1
command to merge a otu_table and tax_table
#1645
Robvh-git
opened
1 year ago
1
How to draw mean value and errorbar using the phyloseq package?
#1644
Kangda384
opened
1 year ago
0
error: data length [] is not a sub-multiple or multiple of the number of rows []
#1643
marwa38
closed
1 year ago
2
rarefy_even depth question
#1642
LaFra7
opened
2 years ago
1
otu_table not working with vegan rarecurve
#1641
ireneadm
opened
2 years ago
5
lines on barplot
#1640
metageno67
opened
2 years ago
2
Possible Feature? estimate_presence?
#1639
mawa86
opened
2 years ago
5
Does anybody work with Reduced Representation Sequencing/GBS data for metagenomic analysis? I have problems creating taxonomic data.
#1638
Pablo-UY
opened
2 years ago
0
plot_tree() queries
#1637
marwa38
opened
2 years ago
3
tax_glom then psmelt centered-log-ratio transformed data?
#1636
gabrielet
opened
2 years ago
1
adding a phy_tree to phyloseq object removes otu_table and tax_table info
#1635
laura-brettell
opened
2 years ago
0
Question about rarefy_even_depth
#1634
LaFra7
opened
2 years ago
0
Any help with bootstrap in the phylogenetic tree?
#1633
marwa38
closed
1 year ago
1
adding phy_tree reduces number of ASVs
#1632
MCK-sketch
opened
2 years ago
0
Combine different markers and have a unique phyloseq object
#1631
LaFra7
opened
2 years ago
0
Fixed paste error in rarefy_even_dept & improved efficiency
#1630
salix-d
opened
2 years ago
1
phyloseq-sample data zero dimensions
#1629
Gigiagio
opened
2 years ago
0
Merging metadata with otu table in a phyloseq object
#1628
lynneitelson
opened
2 years ago
1
Custom x axis labels with plot_bar
#1627
aravenscraft
opened
2 years ago
1
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