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phyloseq
•
reset
0
votes
0
replies
31
views
Association between ohylum and genus on microbiome data sets.
phyloseq
12 days ago
Edmond
• 0
0
votes
0
replies
94
views
How to pool phyloseq data?
phyloseq
r
updated 8 weeks ago by
Michael Love
36k • written 8 weeks ago by
strep
• 0
0
votes
4
replies
203
views
Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings
phyloseq
updated 9 weeks ago by
James W. MacDonald
59k • written 9 weeks ago by
Eman
• 0
0
votes
1
reply
166
views
Deseq workflow for phyloseq object and complicated data structure?
phyloseq
DESeq2
updated 3 months ago by
Michael Love
36k • written 4 months ago by
dschnitzler
• 0
0
votes
4
replies
349
views
Cannot install Phyloseq and dada2
GenomeInfoDbData
phyloseq
dada2
4 months ago • updated 3 months ago
ymtan
• 0
0
votes
1
reply
145
views
Error in 'differential_abundance'
phyloseq
devtools
updated 4 months ago by
Michael Love
36k • written 4 months ago by
strep
• 0
0
votes
1
reply
250
views
convert default phylip to sequential phylip
phyloseq
Phylogenetics
updated 4 months ago by
Arnold
• 0 • written 8 months ago by
memy
• 0
0
votes
0
replies
203
views
Construct a phyloseq object directly from the dada2 outputs
phyloseq
dada2
9 months ago
Manijeh
• 0
0
votes
3
replies
258
views
DESeq2: difficulty with contrasts and main effects
DESeq2
phyloseq
contrasts
updated 9 months ago by
Kevin Blighe
3.5k • written 9 months ago by
Mir
• 0
0
votes
5
replies
1.8k
views
Problems with installation of 'phyloseq
phyloseq
updated 9 months ago by
Kevin Blighe
3.5k • written 9 months ago by
Ina
• 0
0
votes
1
reply
205
views
Purpose of seqtabNoC
phyloseq
updated 10 months ago by
Kevin Blighe
3.5k • written 10 months ago by
klltnq
• 0
0
votes
0
replies
183
views
Construct Phylogenetic Tree
phyloseq
10 months ago
klltnq
• 0
0
votes
0
replies
176
views
Code Issue
phyloseq
10 months ago
klltnq
• 0
0
votes
3
replies
242
views
Installing Packages repeatedly
phyloseq
updated 10 months ago by
Kevin Blighe
3.5k • written 10 months ago by
klltnq
• 0
0
votes
1
reply
655
views
Import MetaPhlAn3 to Phyloseq
Metaphlan3
Metagenomics
phyloseq
updated 10 months ago by
Levi Waldron
1.1k • written 10 months ago by
Saraswati
• 0
1
vote
1
reply
1.1k
views
Setting up bioconductor on a Linux server using conda
dada2
conda
phyloseq
updated 13 months ago by
James W. MacDonald
59k • written 13 months ago by
Daniel
• 0
1
vote
3
replies
341
views
How to assign random effect factor in DESeq2 desing?
StatisticalMethod
DESeq2
phyloseq
updated 15 months ago by
Michael Love
36k • written 15 months ago by
zardbid
• 0
4
votes
3
replies
413
views
Paired-test between two groups within a condition after phyloseq_to_deseq2
DESeq2
phyloseq
updated 15 months ago by
Michael Love
36k • written 15 months ago by
trichorico
▴ 10
0
votes
0
replies
398
views
Co-occurrence Network Analysis between Algae and Bacteria
igraph
networkanalysis
Phylogenetics
phyloseq
16 months ago
Chantel
• 0
1
vote
2
replies
1.1k
views
Bioconductor install error
phyloseq
Bioconductor
18 months ago
Tess
• 0
2
votes
2
replies
566
views
Bioconductor phyloseq taking forever to install?
Bioconductor
phyloseq
18 months ago
garfield320
▴ 30
0
votes
1
reply
537
views
Can I use pseudocounts for differential abundance of OTUs?
metagenomics
deseq2
PHYLOSEQ
updated 21 months ago by
Michael Love
36k • written 21 months ago by
dc
• 0
0
votes
2
replies
418
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
22 months ago
jaiber.solano.i
• 0
0
votes
3
replies
357
views
Nested design- phyloseq_to_deseq
deseq2
Phyloseq
Nested
updated 2.1 years ago by
Michael Love
36k • written 2.1 years ago by
mpuli011
• 0
0
votes
2
replies
1.8k
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 2.4 years ago by
Martin Morgan
25k • written 2.4 years ago by
crgarcia
• 0
0
votes
0
replies
383
views
Problems with creating phyloseq bar plots from a table with species data
phyloseq
microbiome analysis
3.3 years ago
lm795
▴ 10
0
votes
2
replies
497
views
Phyloseq to DESeq2
deseq2
phyloseq
updated 3.3 years ago by
Michael Love
36k • written 3.3 years ago by
staffordvigors
• 0
0
votes
1
reply
786
views
Import_biom with tree problem
phyloseq
mothur
16s
3.6 years ago
andrebolerbarros
▴ 10
5
votes
11
replies
1.8k
views
Error while installing Phyloseq using biocLite
bioclite
phyloseq
install error
3.6 years ago
khp
▴ 30
0
votes
9
replies
1.2k
views
DESEQ2 / Phyloseq contrasts no longer work as before following update
deseq2
phyloseq
3.7 years ago
eoin
• 0
0
votes
1
reply
445
views
Invalid class DESeqDataSet object with Phyloseq
deseq2
phyloseq
updated 3.8 years ago by
Michael Love
36k • written 3.8 years ago by
amgodogma
▴ 10
0
votes
1
reply
834
views
Install package phyloseq
installation
phyloseq
updated 4.2 years ago by
Martin Morgan
25k • written 4.2 years ago by
layeb
• 0
0
votes
1
reply
795
views
tip_glom and annotations?
ggtree
treeio
phyloseq
annotation
tip_glom
updated 4.3 years ago by
Guangchuang Yu
★ 1.2k • written 4.3 years ago by
werdnus
• 0
1
vote
1
reply
811
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2
R
microbiome
phyloseq
qiime
updated 4.5 years ago by
Michael Love
36k • written 4.5 years ago by
ssingh59
• 0
1
vote
8
replies
3.4k
views
Cannot read Biom file
r
biomformat
phyloseq
updated 4.5 years ago by
Axel Klenk
▴ 990 • written 4.5 years ago by
channen1221
• 0
0
votes
0
replies
624
views
Problem with ade4 when upgrading to Rstudio 1.1 and OpenR 3.4
phyloseq
installation
ade4
macos
4.6 years ago
sprague
• 0
2
votes
2
replies
1.9k
views
DESeq2 iterative size factor normalization did not converge
deseq2
microbiome
phyloseq
updated 4.7 years ago by
Michael Love
36k • written 4.7 years ago by
couchc
• 0
0
votes
1
reply
748
views
phyloseq heatmap blank after multiple package updates
phyloseq
heatmap
updated 4.7 years ago by
Wolfgang Huber
13k • written 4.7 years ago by
newmanss
• 0
1
vote
3
replies
1.1k
views
Error bars on DESeq2 visuals
deseq2
metagenomics
phyloseq
ggplot2
4.7 years ago
lauren.czaplicki
• 0
0
votes
1
reply
913
views
Phyloseq to DESeq2 with multiple variables
deseq2
phyloseq
multiple time points
updated 4.8 years ago by
Michael Love
36k • written 4.8 years ago by
campbell87
• 0
0
votes
0
replies
752
views
Phylogenetic tree from marker genes
ape
phyloseq
dist
metagenomics
5.1 years ago
David
▴ 860
1
vote
1
reply
2.2k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome
normalization
variancestabilizingtransformation
phyloseq
5.1 years ago
stats134711
• 0
0
votes
1
reply
1.4k
views
ggtree facet_plot question using geom_boxplot to plot abundance data corresponding to tree tips
ggtree
ggplot2
phyloseq
geom_boxplot
facet_plot
updated 5.2 years ago by
Guangchuang Yu
★ 1.2k • written 5.2 years ago by
matthew.wipperman
• 0
2
votes
2
replies
1.0k
views
DESeq2 in phyloseq
deseq2
phyloseq
5.2 years ago
sarahmacdonald86
• 0
0
votes
2
replies
1.2k
views
Controlling colours assigned to order in DeSeq2 plot in phyloseq
phyloseq
color
ggplot2
updated 5.2 years ago by
Michael Love
36k • written 5.2 years ago by
sarahmacdonald86
• 0
1
vote
2
replies
944
views
rlogTransformation vs getVarianceStabilizedData
deseq2
r
phyloseq
updated 5.5 years ago by
Michael Love
36k • written 5.5 years ago by
fabian.roger08
▴ 10
0
votes
0
replies
1.4k
views
Error with phyloseq R package with Conda install
software error
phyloseq
anaconda
5.5 years ago
kpitz23
• 0
0
votes
1
reply
1.3k
views
phyloseq biom json format conversion needed to hdf5 format for qiime
biom
json
hdf5
qiime
phyloseq
updated 5.5 years ago by
Bernd Fischer
▴ 550 • written 5.6 years ago by
newmanss
• 0
0
votes
1
reply
1.5k
views
phyloseq merge_samples attempt to set rownames on an object with no dimensions
phyloseq
merge_samples
rownames
error
5.6 years ago
newmanss
• 0
0
votes
3
replies
1.1k
views
DESeq2 blocking by condition over time
deseq2
phyloseq
time course
5.7 years ago
akp
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: TPM data Differential expression analysis
by
hnthirim
▴ 10
Hi @gordonsmyth, Question on your above answer: I have logTPM normalized data. Can I perform DE analysis using it on EdgeR, instead of in…
Comment: rtracklayer S.h
by
gibran
• 0
Thanks, much appreciated. So I think this approach actually gets binaries and I'm not sure how to isolate the problem I was experiencing as…
Comment: DESeq2, Calculate the size factor by using median-of-ratio
by
KEREN
• 0
Hi Michael, thank you for you reply. My concern here mainly focus on the high variances in samples of condition "mESC_mRNA_WT". I observed…
Comment: DiffBind: 0 consensus peaks for dba.peakset: New bug / undocumented change intro
by
Rory Stark
★ 4.4k
I agree the documentation could be clearer -- it took me a while to understand what it said so I could address your issue!
Answer: DiffBind: 0 consensus peaks for dba.peakset: New bug / undocumented change intro
by
chrarnold
• 0
Thanks a lot for your quick reply, it is very appreciated! Indeed, with your 2 suggested modifications, I can again reproduce the results f…
Votes
Answer: rtracklayer S.h
Answer: rtracklayer S.h
Answer: DESeq2: Extracting Averaged Counts Information from dds and rld
Answer: DESeq2: Extracting Averaged Counts Information from dds and rld
Answer: DESeq2: Extracting Averaged Counts Information from dds and rld
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