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Showing :
phyloseq
•
reset
5
votes
11
replies
2.8k
views
Error while installing Phyloseq using biocLite
bioclite
phyloseq
install error
5.6 years ago
khp
▴ 30
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
3
votes
2
replies
2.1k
views
DESEQ2 (R) design/contrast formula questions
deseq2
phyloseq
multiple factor design
paired samples
updated 8.1 years ago by
mcmurdie
▴ 20 • written 8.1 years ago by
pete_bioinfo
▴ 10
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
2
votes
2
replies
1.5k
views
DESeq2 in phyloseq
deseq2
phyloseq
7.1 years ago
sarahmacdonald86
• 0
2
votes
9
replies
20k
views
Error in file(con, “r”) : cannot open the connection
r
phyloseq
import_biom
otu
qiime
updated 8.5 years ago by
mcmurdie
▴ 20 • written 8.5 years ago by
moanam
• 0
2
votes
2
replies
1.5k
views
Bioconductor phyloseq taking forever to install?
Bioconductor
phyloseq
3.5 years ago
garfield320
▴ 30
2
votes
2
replies
6.3k
views
Interpretation of intercept-only model (~1) in DESeq2
deseq2
phyloseq
updated 8.2 years ago by
Michael Love
41k • written 8.2 years ago by
piensaglobalmente
▴ 10
2
votes
1
reply
994
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
2
votes
1
reply
1.9k
views
Using DESeq2 after agglomerating OTUs
phyloseq
deseq2
estimatesizefactors
updated 8.4 years ago by
Michael Love
41k • written 8.4 years ago by
brandilyn.peters
• 0
1
vote
8
replies
5.9k
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
1
vote
1
reply
3.5k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome
normalization
variancestabilizingtransformation
phyloseq
7.0 years ago
stats134711
• 0
1
vote
2
replies
2.3k
views
Bioconductor install error
phyloseq
Bioconductor
3.4 years ago
Tess
• 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
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
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
1
reply
2.5k
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
1
vote
3
replies
1.9k
views
Error bars on DESeq2 visuals
deseq2
metagenomics
phyloseq
ggplot2
6.7 years ago
lauren.czaplicki
• 0
1
vote
10
replies
2.3k
views
Multi-factor Comparison in DESeq 2 Issue
deseq2
phyloseq
updated 9.2 years ago by
Ryan C. Thompson
★ 7.9k • written 9.2 years ago by
locon833
• 0
1
vote
2
replies
2.1k
views
DESeqs two-factor two-level, interaction is interested
Sequencing
GO
phyloseq
DESeq2
Sequencing
GO
phyloseq
DESeq2
updated 9.8 years ago by
Michael Love
41k • written 9.8 years ago by
Shucong Li
▴ 60
1
vote
2
replies
1.4k
views
rlogTransformation vs getVarianceStabilizedData
deseq2
r
phyloseq
updated 7.4 years ago by
Michael Love
41k • written 7.4 years ago by
fabian.roger08
▴ 10
0
votes
1
reply
1.6k
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
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
837
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
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
1.5k
views
Import_biom with tree problem
phyloseq
mothur
16s
5.5 years ago
andrebolerbarros
▴ 20
0
votes
2
replies
972
views
Phyloseq to DESeq2
deseq2
phyloseq
updated 5.3 years ago by
Michael Love
41k • written 5.3 years ago by
staffordvigors
• 0
0
votes
0
replies
821
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
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 4.4 years ago by
Martin Morgan
25k • written 4.4 years ago by
crgarcia
• 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
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
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
1
reply
683
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 14 days ago by
President Gamer
• 0 • written 10 months ago by
abhisek001
• 0
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
0
votes
1
reply
661
views
error installing phyloseq
phyloseq
updated 22 months ago by
shepherl
3.8k • written 22 months ago by
Ezra
• 0
0
votes
0
replies
762
views
Construct a phyloseq object directly from the dada2 outputs
phyloseq
dada2
2.7 years ago
Manijeh
• 0
0
votes
1
reply
2.2k
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
0
votes
4
replies
1.8k
views
Cannot install Phyloseq and dada2
GenomeInfoDbData
phyloseq
dada2
2.3 years ago
ymtan
• 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
759
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
3
replies
874
views
Controversial DESEQ2 results
phyloseq
DESeq2
updated 22 months ago by
Michael Love
41k • written 23 months ago by
Stephan
• 0
0
votes
3
replies
769
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
685
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
0
replies
620
views
Code Issue
phyloseq
2.8 years ago
klltnq
• 0
0
votes
0
replies
726
views
Construct Phylogenetic Tree
phyloseq
2.8 years ago
klltnq
• 0
0
votes
5
replies
6.4k
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
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
3
replies
1.0k
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
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
496
views
Association between ohylum and genus on microbiome data sets.
phyloseq
24 months ago
Edmond
• 0
50 results • Page
1 of 1
Recent ...
Replies
Answer: Dominance Index for Shotgun Metagenomics Data
by
Leo Lahti
▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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