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Phyloseq
•
reset
2
votes
1
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981
views
Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq
microbiome
Software
updated 7 months ago by
ATpoint
★ 4.0k • written 7 months ago by
HULFRED
▴ 10
0
votes
0
replies
353
views
Try to understand better how to set out an effective sample size within the MetagenomSeq package in microbiome ?
Metagenomics
metagenomeSeq
microbiome
phyloseq
microbiomeDataSets
8 months ago
Mohamed
▴ 30
0
votes
1
reply
677
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 10 days ago by
President Gamer
• 0 • written 10 months ago by
abhisek001
• 0
1
vote
1
reply
2.4k
views
does anyone how to create rarefaction curves from a phyloseq object?
phyloseq
Phylogenetics
updated 13 months ago by
RMiller
▴ 10 • written 13 months ago by
kevin
• 0
0
votes
3
replies
1.6k
views
I cannot install "microbiome"
GenomeInfoDbData
microbiome
phyloseq
updated 20 months ago by
Marcel Ramos
690 • written 20 months ago by
kikiki
• 0
0
votes
1
reply
657
views
error installing phyloseq
phyloseq
updated 22 months ago by
shepherl
3.8k • written 22 months ago by
Ezra
• 0
0
votes
3
replies
868
views
Controversial DESEQ2 results
phyloseq
DESeq2
updated 22 months ago by
Michael Love
41k • written 23 months ago by
Stephan
• 0
0
votes
0
replies
491
views
Association between ohylum and genus on microbiome data sets.
phyloseq
23 months ago
Edmond
• 0
0
votes
0
replies
1.3k
views
How to pool phyloseq data?
phyloseq
r
updated 2.1 years ago by
Michael Love
41k • written 2.1 years ago by
strep
• 0
0
votes
4
replies
1.8k
views
Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings
phyloseq
updated 2.1 years ago by
James W. MacDonald
65k • written 2.1 years ago by
Eman
• 0
0
votes
1
reply
754
views
Deseq workflow for phyloseq object and complicated data structure?
phyloseq
DESeq2
updated 2.3 years ago by
Michael Love
41k • written 2.3 years ago by
dschnitzler
• 0
0
votes
4
replies
1.8k
views
Cannot install Phyloseq and dada2
GenomeInfoDbData
phyloseq
dada2
2.3 years ago
ymtan
• 0
0
votes
1
reply
681
views
Error in 'differential_abundance'
phyloseq
devtools
updated 2.3 years ago by
Michael Love
41k • written 2.3 years ago by
strep
• 0
0
votes
6
replies
1.4k
views
convert default phylip to sequential phylip
phyloseq
Phylogenetics
updated 12 months ago by
yrkkhdesiserials
• 0 • written 2.7 years ago by
memy
• 0
0
votes
0
replies
759
views
Construct a phyloseq object directly from the dada2 outputs
phyloseq
dada2
2.7 years ago
Manijeh
• 0
0
votes
3
replies
996
views
DESeq2: difficulty with contrasts and main effects
DESeq2
phyloseq
contrasts
updated 2.7 years ago by
Kevin Blighe
★ 3.9k • written 2.7 years ago by
Mir
• 0
0
votes
5
replies
6.3k
views
Problems with installation of 'phyloseq
phyloseq
updated 2.7 years ago by
Kevin Blighe
★ 3.9k • written 2.7 years ago by
Ina
• 0
0
votes
0
replies
724
views
Construct Phylogenetic Tree
phyloseq
2.8 years ago
klltnq
• 0
0
votes
0
replies
618
views
Code Issue
phyloseq
2.8 years ago
klltnq
• 0
0
votes
1
reply
684
views
Purpose of seqtabNoC
phyloseq
updated 2.8 years ago by
Kevin Blighe
★ 3.9k • written 2.8 years ago by
klltnq
• 0
0
votes
3
replies
762
views
Installing Packages repeatedly
phyloseq
updated 2.8 years ago by
Kevin Blighe
★ 3.9k • written 2.8 years ago by
klltnq
• 0
0
votes
1
reply
2.1k
views
Import MetaPhlAn3 to Phyloseq
Metaphlan3
Metagenomics
phyloseq
updated 2.8 years ago by
Levi Waldron
★ 1.1k • written 2.8 years ago by
Saraswati
• 0
1
vote
1
reply
3.6k
views
Setting up bioconductor on a Linux server using conda
dada2
conda
phyloseq
updated 3.1 years ago by
James W. MacDonald
65k • written 3.1 years ago by
Daniel
• 0
1
vote
3
replies
1.1k
views
How to assign random effect factor in DESeq2 desing?
StatisticalMethod
DESeq2
phyloseq
updated 3.2 years ago by
Michael Love
41k • written 3.2 years ago by
zardbid
• 0
4
votes
3
replies
1.1k
views
Paired-test between two groups within a condition after phyloseq_to_deseq2
DESeq2
phyloseq
updated 3.2 years ago by
Michael Love
41k • written 3.2 years ago by
trichorico
▴ 10
0
votes
0
replies
1.1k
views
Co-occurrence Network Analysis between Algae and Bacteria
igraph
networkanalysis
Phylogenetics
phyloseq
3.3 years ago
Chantel
• 0
1
vote
2
replies
2.3k
views
Bioconductor install error
phyloseq
Bioconductor
3.4 years ago
Tess
• 0
2
votes
2
replies
1.5k
views
Bioconductor phyloseq taking forever to install?
Bioconductor
phyloseq
3.5 years ago
garfield320
▴ 30
0
votes
1
reply
1.1k
views
Can I use pseudocounts for differential abundance of OTUs?
metagenomics
deseq2
PHYLOSEQ
updated 3.7 years ago by
Michael Love
41k • written 3.7 years ago by
dc
• 0
0
votes
2
replies
1.9k
views
Error in taxa_are_rows(x) : trying to get slot "taxa_are_rows" from an object (class "otu_table") that is not an S4 object
deseq2
phyloseq
3.8 years ago
jaiber.solano.i
• 0
0
votes
3
replies
1.0k
views
Nested design- phyloseq_to_deseq
deseq2
Phyloseq
Nested
updated 4.1 years ago by
Michael Love
41k • written 4.1 years ago by
mpuli011
• 0
0
votes
2
replies
2.9k
views
Problems with bioconductor after updating R to 3.6.2
R 3.6.2 update problems with igraph and phangorn update
Phyloseq
igraph
phangorn
Tutorial
updated 4.3 years ago by
Martin Morgan
25k • written 4.3 years ago by
crgarcia
• 0
0
votes
0
replies
818
views
Problems with creating phyloseq bar plots from a table with species data
phyloseq
microbiome analysis
5.2 years ago
lm795
▴ 10
0
votes
2
replies
969
views
Phyloseq to DESeq2
deseq2
phyloseq
updated 5.2 years ago by
Michael Love
41k • written 5.3 years ago by
staffordvigors
• 0
0
votes
1
reply
1.5k
views
Import_biom with tree problem
phyloseq
mothur
16s
5.5 years ago
andrebolerbarros
▴ 20
5
votes
11
replies
2.7k
views
Error while installing Phyloseq using biocLite
bioclite
phyloseq
install error
5.5 years ago
khp
▴ 30
0
votes
9
replies
2.4k
views
DESEQ2 / Phyloseq contrasts no longer work as before following update
deseq2
phyloseq
5.6 years ago
eoin
• 0
0
votes
1
reply
833
views
Invalid class DESeqDataSet object with Phyloseq
deseq2
phyloseq
updated 5.7 years ago by
Michael Love
41k • written 5.7 years ago by
amgodogma
▴ 10
0
votes
1
reply
1.7k
views
Install package phyloseq
installation
phyloseq
updated 6.1 years ago by
Martin Morgan
25k • written 6.1 years ago by
layeb
• 0
0
votes
1
reply
1.5k
views
tip_glom and annotations?
ggtree
treeio
phyloseq
annotation
tip_glom
updated 6.2 years ago by
Guangchuang Yu
★ 1.2k • written 6.2 years ago by
werdnus
• 0
1
vote
1
reply
1.4k
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2
R
microbiome
phyloseq
qiime
updated 6.4 years ago by
Michael Love
41k • written 6.4 years ago by
ssingh59
• 0
1
vote
8
replies
5.8k
views
Cannot read Biom file
r
biomformat
phyloseq
updated 6.5 years ago by
Axel Klenk
★ 1.0k • written 6.5 years ago by
channen1221
• 0
0
votes
0
replies
1.2k
views
Problem with ade4 when upgrading to Rstudio 1.1 and OpenR 3.4
phyloseq
installation
ade4
macos
6.5 years ago
sprague
• 0
3
votes
2
replies
3.3k
views
DESeq2 iterative size factor normalization did not converge
deseq2
microbiome
phyloseq
updated 6.6 years ago by
Michael Love
41k • written 6.6 years ago by
couchc
• 0
0
votes
1
reply
1.3k
views
phyloseq heatmap blank after multiple package updates
phyloseq
heatmap
updated 6.6 years ago by
Wolfgang Huber
★ 13k • written 6.6 years ago by
newmanss
• 0
1
vote
3
replies
1.9k
views
Error bars on DESeq2 visuals
deseq2
metagenomics
phyloseq
ggplot2
6.7 years ago
lauren.czaplicki
• 0
0
votes
1
reply
1.5k
views
Phyloseq to DESeq2 with multiple variables
deseq2
phyloseq
multiple time points
updated 6.8 years ago by
Michael Love
41k • written 6.8 years ago by
campbell87
• 0
0
votes
0
replies
1.3k
views
Phylogenetic tree from marker genes
ape
phyloseq
dist
metagenomics
7.0 years ago
David
▴ 860
1
vote
1
reply
3.5k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome
normalization
variancestabilizingtransformation
phyloseq
7.0 years ago
stats134711
• 0
0
votes
1
reply
2.0k
views
ggtree facet_plot question using geom_boxplot to plot abundance data corresponding to tree tips
ggtree
ggplot2
phyloseq
geom_boxplot
facet_plot
updated 7.1 years ago by
Guangchuang Yu
★ 1.2k • written 7.1 years ago by
matthew.wipperman
• 0
50 results • Page
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Replies
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Seyram M.
• 0
Dear Michael, I tried all three ways (the orIginal, increasing the number of required samples,and subsetting (the countdata and metadata be…
Comment: DESeq2 - dispersion estimation when there is none
by
Michael Love
41k
The red line does assume that shape but the fact the black points show that pattern is discussed in the 2014 paper. > Some caution is warr…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function
by
James W. MacDonald
65k
I don't really follow what you are saying. All you have to do is delete the NCBI.sqlite db and *re-run the script exactly as you did above.…
Comment: Methylation Analysis experiment design using Limma
by
hortense96
• 0
Thank you very much for your reply and your suggestion, as I'm having a bit of trouble finding information on how to manage this part of th…
Comment: Limma design with continuous and categorical covariates
by
hortense96
• 0
Hello, I'm trying to do a differential methylation analysis with the Limma package and was wondering if you had any suggestions on how to …
Votes
Comment: DESeq2 - dispersion estimation when there is none
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
Answer: OrgDb for maize
Answer: DESeq2 - dispersion estimation when there is none
Comment: Cannabis and KEGGgraph
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