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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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Change in internal nodes when appending phylogenetic tree to phyloseq
#1622
LaraMacheriotou
opened
2 years ago
0
sam_data slot is empty
#1621
lynneitelson
opened
2 years ago
5
Error in access(object, "sam_data", errorIfNULL) : sam_data slot is empty.
#1620
B-1991-ing
opened
2 years ago
9
Tax glom not operating on phyloseq object
#1619
paddyhooper
opened
2 years ago
7
plot_ordination() visualisation query?
#1618
marwa38
closed
1 year ago
4
Filter ASV according to each group
#1617
YuZhang-learner
opened
2 years ago
0
How to rank by Relative Abundance? Why are values greater than 1?
#1616
sarakn97
opened
2 years ago
1
tax_table function stopped working properly
#1615
valentinavan
opened
2 years ago
3
How to Identify Top 10 Most Abundant Fungi Genera and list them with Relative Abundance.
#1614
sarakn97
opened
2 years ago
2
plot_ordination of ordinate result using CAP gives axis1 = CAP1 and axis2 = MDS1
#1613
MirjamBloem
opened
2 years ago
9
Request to add additional aes() arguments to plot_ordination
#1612
gcuster1991
closed
2 years ago
5
UniFrac distances not working after merging samples
#1611
ibrila
closed
2 years ago
1
TSNE and UMAP and 3D
#1610
pedrocr83
opened
2 years ago
0
pairwise.adonis2 result is not consistent with the result of adonis2
#1609
holly2021FL
opened
2 years ago
2
To compare the OTU method with the ASV method
#1608
MDSHAHADATHOSSAIN
opened
2 years ago
3
write_phyloseq does not work in R4.2.1
#1607
brockels
opened
2 years ago
2
tax_glom problem
#1606
aff30
opened
2 years ago
1
Strange barplot results
#1605
rick8813
opened
2 years ago
0
total number of taxa even after subsetting?!
#1604
marwa38
closed
1 year ago
4
OTU Table Formating
#1603
NaomiHuntley
opened
2 years ago
1
Create a HeatMap at the genus level
#1602
ghost
closed
1 year ago
1
Density plot
#1601
valentinavan
closed
2 years ago
1
Calculate the average of the relative abundance at Family level
#1600
cabraham03
opened
2 years ago
4
phyloseq function drops variables
#1599
valentinavan
closed
2 years ago
0
tax_glom, invalid archetype provided
#1598
chuynh96
opened
2 years ago
2
Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘tax_table’ for signature ‘"matrix"’
#1597
Gowri1994
opened
2 years ago
6
Potential error in phyloseq::rarefy_even_depth
#1596
Pstege
opened
2 years ago
1
Rarefy and Restroom example
#1595
mweberr
opened
2 years ago
1
How to convert the results from USEARCH to phyloseq object?
#1594
paiboon-aut
opened
2 years ago
0
Need to calculate top taxa by sample
#1593
pauGuas
opened
2 years ago
1
Importing atypical data
#1592
lauramason326
opened
2 years ago
1
Importing sequence file to existing phyloseq object
#1591
act837
closed
2 years ago
2
filtering step
#1590
aff30
opened
2 years ago
2
How to import metaphlan style in phyloseq
#1589
BaylorLyu
opened
2 years ago
1
Merge new data with current phyloseq object
#1588
jajarom16
opened
2 years ago
1
Extract Alpha Diversity Output into excel or .csv file
#1587
vee3capp
opened
2 years ago
1
Barplot of relative abundance for a longitudinal study
#1586
otaviolovison
opened
2 years ago
1
Error when making phyloseq object
#1585
Callahan-McG
closed
2 years ago
1
Taxa bar plot issue (taxa are not arranged as per their percentages) fct_reorder not working
#1584
ghost
closed
2 years ago
0
tax_glom() not aggregating with no error message
#1583
Callahan-McG
closed
2 years ago
2
fisher.alpha(x, se=TRUE) is defunct since Dec 2013: can cause error
#1582
jarioksa
opened
2 years ago
0
se=TRUE has been unavailable in vegan::fisher.alpha since 2013
#1581
jarioksa
opened
2 years ago
2
Components of differing sample lengths
#1580
jmlayton
opened
2 years ago
1
Error when calculating prevalence of taxa (arguments imply differing number of rows)
#1579
emankhalaf
opened
2 years ago
2
Issue merging phyloseq objects
#1578
pauGuas
closed
2 years ago
1
Error for merging phylogenetic tree in phyloseq object from Kraken2 + Bracken output
#1577
magibc
closed
2 years ago
1
phyla overlapped between two groups
#1576
marwa38
opened
2 years ago
0
Calculate and plot 10 most abundant taxa?
#1575
LaFra7
opened
2 years ago
5
why "not a sub-multiple or multiple of the number of rows" appreared at Unifrac?
#1574
wanglu2014
opened
2 years ago
1
Error when extracting genera sequences at 50% prevalence threshold
#1573
emankhalaf
closed
2 years ago
0
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