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Phyloseq
•
reset
5
votes
11
replies
2.8k
views
Error while installing Phyloseq using biocLite
bioclite
phyloseq
install error
5.5 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
6.2k
views
Interpretation of intercept-only model (~1) in DESeq2
deseq2
phyloseq
updated 8.1 years ago by
Michael Love
41k • written 8.1 years ago by
piensaglobalmente
▴ 10
2
votes
1
reply
988
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
1.5k
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
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
836
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
971
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
820
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
682
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 12 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
659
views
error installing phyloseq
phyloseq
updated 22 months ago by
shepherl
3.8k • written 22 months ago by
Ezra
• 0
0
votes
0
replies
761
views
Construct a phyloseq object directly from the dada2 outputs
phyloseq
dada2
2.7 years ago
Manijeh
• 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
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
757
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
870
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
766
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
619
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
1000
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
494
views
Association between ohylum and genus on microbiome data sets.
phyloseq
24 months ago
Edmond
• 0
50 results • Page
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Recent ...
Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre
Comment: How to retrieve gene ontology GO class from gene list?
by
James W. MacDonald
65k
Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…
Comment: How to retrieve gene ontology GO class from gene list?
by
bandconductor
• 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
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