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Showing :
PHYLOSEQ
•
reset
2
votes
1
reply
405
views
Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq
microbiome
Software
updated 10 weeks ago by
ATpoint
★ 3.6k • written 10 weeks ago by
HULFRED
▴ 10
0
votes
0
replies
207
views
Try to understand better how to set out an effective sample size within the MetagenomSeq package in microbiome ?
Metagenomics
metagenomeSeq
microbiome
phyloseq
microbiomeDataSets
3 months ago
Mohamed
▴ 20
0
votes
1
reply
349
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
written 5 months ago by
abhisek001
• 0
0
votes
6
replies
1.2k
views
convert default phylip to sequential phylip
phyloseq
Phylogenetics
updated 7 months ago by
yrkkhdesiserials
• 0 • written 2.3 years ago by
memy
• 0
1
vote
1
reply
1.5k
views
does anyone how to create rarefaction curves from a phyloseq object?
phyloseq
Phylogenetics
updated 8 months ago by
RMiller
▴ 10 • written 8 months ago by
kevin
• 0
0
votes
3
replies
1.2k
views
I cannot install "microbiome"
GenomeInfoDbData
microbiome
phyloseq
updated 15 months ago by
Marcel Ramos
680 • written 15 months ago by
kikiki
• 0
0
votes
1
reply
528
views
error installing phyloseq
phyloseq
updated 17 months ago by
shepherl
3.6k • written 17 months ago by
Ezra
• 0
0
votes
3
replies
716
views
Controversial DESEQ2 results
phyloseq
DESeq2
updated 18 months ago by
Michael Love
41k • written 18 months ago by
Stephan
• 0
0
votes
0
replies
392
views
Association between ohylum and genus on microbiome data sets.
phyloseq
19 months ago
Edmond
• 0
0
votes
0
replies
1.1k
views
How to pool phyloseq data?
phyloseq
r
updated 20 months ago by
Michael Love
41k • written 20 months ago by
strep
• 0
0
votes
4
replies
1.4k
views
Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings
phyloseq
updated 20 months ago by
James W. MacDonald
64k • written 20 months ago by
Eman
• 0
0
votes
1
reply
641
views
Deseq workflow for phyloseq object and complicated data structure?
phyloseq
DESeq2
updated 22 months ago by
Michael Love
41k • written 22 months ago by
dschnitzler
• 0
0
votes
4
replies
1.5k
views
Cannot install Phyloseq and dada2
GenomeInfoDbData
phyloseq
dada2
22 months ago
ymtan
• 0
0
votes
1
reply
556
views
Error in 'differential_abundance'
phyloseq
devtools
updated 23 months ago by
Michael Love
41k • written 23 months ago by
strep
• 0
0
votes
0
replies
646
views
Construct a phyloseq object directly from the dada2 outputs
phyloseq
dada2
2.3 years ago
Manijeh
• 0
0
votes
3
replies
823
views
DESeq2: difficulty with contrasts and main effects
DESeq2
phyloseq
contrasts
updated 2.3 years ago by
Kevin Blighe
3.9k • written 2.3 years ago by
Mir
• 0
0
votes
5
replies
5.4k
views
Problems with installation of 'phyloseq
phyloseq
updated 2.3 years ago by
Kevin Blighe
3.9k • written 2.3 years ago by
Ina
• 0
0
votes
1
reply
580
views
Purpose of seqtabNoC
phyloseq
updated 2.4 years ago by
Kevin Blighe
3.9k • written 2.4 years ago by
klltnq
• 0
0
votes
0
replies
608
views
Construct Phylogenetic Tree
phyloseq
2.4 years ago
klltnq
• 0
0
votes
0
replies
524
views
Code Issue
phyloseq
2.4 years ago
klltnq
• 0
0
votes
3
replies
657
views
Installing Packages repeatedly
phyloseq
updated 2.4 years ago by
Kevin Blighe
3.9k • written 2.4 years ago by
klltnq
• 0
0
votes
1
reply
1.8k
views
Import MetaPhlAn3 to Phyloseq
Metaphlan3
Metagenomics
phyloseq
updated 2.4 years ago by
Levi Waldron
1.1k • written 2.4 years ago by
Saraswati
• 0
1
vote
1
reply
3.1k
views
Setting up bioconductor on a Linux server using conda
dada2
conda
phyloseq
updated 2.7 years ago by
James W. MacDonald
64k • written 2.7 years ago by
Daniel
• 0
1
vote
3
replies
912
views
How to assign random effect factor in DESeq2 desing?
StatisticalMethod
DESeq2
phyloseq
updated 2.8 years ago by
Michael Love
41k • written 2.8 years ago by
zardbid
• 0
4
votes
3
replies
956
views
Paired-test between two groups within a condition after phyloseq_to_deseq2
DESeq2
phyloseq
updated 2.8 years ago by
Michael Love
41k • written 2.8 years ago by
trichorico
▴ 10
0
votes
0
replies
917
views
Co-occurrence Network Analysis between Algae and Bacteria
igraph
networkanalysis
Phylogenetics
phyloseq
2.9 years ago
Chantel
• 0
1
vote
2
replies
2.0k
views
Bioconductor install error
phyloseq
Bioconductor
3.0 years ago
Tess
• 0
2
votes
2
replies
1.3k
views
Bioconductor phyloseq taking forever to install?
Bioconductor
phyloseq
3.1 years ago
garfield320
▴ 30
0
votes
1
reply
983
views
Can I use pseudocounts for differential abundance of OTUs?
metagenomics
deseq2
PHYLOSEQ
updated 3.3 years ago by
Michael Love
41k • written 3.3 years ago by
dc
• 0
0
votes
2
replies
1.6k
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
3.4 years ago
jaiber.solano.i
• 0
0
votes
3
replies
865
views
Nested design- phyloseq_to_deseq
deseq2
Phyloseq
Nested
updated 3.7 years ago by
Michael Love
41k • written 3.7 years ago by
mpuli011
• 0
0
votes
2
replies
2.6k
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 3.9 years ago by
Martin Morgan
25k • written 3.9 years ago by
crgarcia
• 0
0
votes
0
replies
706
views
Problems with creating phyloseq bar plots from a table with species data
phyloseq
microbiome analysis
4.8 years ago
lm795
▴ 10
0
votes
2
replies
866
views
Phyloseq to DESeq2
deseq2
phyloseq
updated 4.9 years ago by
Michael Love
41k • written 4.9 years ago by
staffordvigors
• 0
0
votes
1
reply
1.3k
views
Import_biom with tree problem
phyloseq
mothur
16s
5.1 years ago
andrebolerbarros
▴ 20
5
votes
11
replies
2.5k
views
Error while installing Phyloseq using biocLite
bioclite
phyloseq
install error
5.1 years ago
khp
▴ 30
0
votes
9
replies
2.2k
views
DESEQ2 / Phyloseq contrasts no longer work as before following update
deseq2
phyloseq
5.2 years ago
eoin
• 0
0
votes
1
reply
705
views
Invalid class DESeqDataSet object with Phyloseq
deseq2
phyloseq
updated 5.3 years ago by
Michael Love
41k • written 5.3 years ago by
amgodogma
▴ 10
0
votes
1
reply
1.5k
views
Install package phyloseq
installation
phyloseq
updated 5.7 years ago by
Martin Morgan
25k • written 5.7 years ago by
layeb
• 0
0
votes
1
reply
1.3k
views
tip_glom and annotations?
ggtree
treeio
phyloseq
annotation
tip_glom
updated 5.8 years ago by
Guangchuang Yu
★ 1.2k • written 5.8 years ago by
werdnus
• 0
1
vote
1
reply
1.2k
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2
R
microbiome
phyloseq
qiime
updated 6.0 years ago by
Michael Love
41k • written 6.0 years ago by
ssingh59
• 0
1
vote
8
replies
5.2k
views
Cannot read Biom file
r
biomformat
phyloseq
updated 6.1 years ago by
Axel Klenk
▴ 990 • written 6.1 years ago by
channen1221
• 0
0
votes
0
replies
1.1k
views
Problem with ade4 when upgrading to Rstudio 1.1 and OpenR 3.4
phyloseq
installation
ade4
macos
6.1 years ago
sprague
• 0
3
votes
2
replies
2.9k
views
DESeq2 iterative size factor normalization did not converge
deseq2
microbiome
phyloseq
updated 6.2 years ago by
Michael Love
41k • written 6.2 years ago by
couchc
• 0
0
votes
1
reply
1.2k
views
phyloseq heatmap blank after multiple package updates
phyloseq
heatmap
updated 6.2 years ago by
Wolfgang Huber
13k • written 6.2 years ago by
newmanss
• 0
1
vote
3
replies
1.7k
views
Error bars on DESeq2 visuals
deseq2
metagenomics
phyloseq
ggplot2
6.3 years ago
lauren.czaplicki
• 0
0
votes
1
reply
1.4k
views
Phyloseq to DESeq2 with multiple variables
deseq2
phyloseq
multiple time points
updated 6.4 years ago by
Michael Love
41k • written 6.4 years ago by
campbell87
• 0
0
votes
0
replies
1.2k
views
Phylogenetic tree from marker genes
ape
phyloseq
dist
metagenomics
6.6 years ago
David
▴ 860
1
vote
1
reply
3.2k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome
normalization
variancestabilizingtransformation
phyloseq
6.6 years ago
stats134711
• 0
0
votes
1
reply
1.9k
views
ggtree facet_plot question using geom_boxplot to plot abundance data corresponding to tree tips
ggtree
ggplot2
phyloseq
geom_boxplot
facet_plot
updated 6.7 years ago by
Guangchuang Yu
★ 1.2k • written 6.7 years ago by
matthew.wipperman
• 0
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Comment: NCBI protein to NCBI cDNA (Ensembl conversions would be great as well) in R
by
James W. MacDonald
64k
It does look like CBP2 is an HGNC symbol, not a protein ID though. ``` > z <- select(ws, "CPB2", c("gene_names","xref_geneid","xref_ensemb…
Comment: How can I avoid artifacts in gene set/pathway scoring by UCell and similar algor
by
arina
• 0
Hi Omer, Unfortunately I don't have an answer to your issue, but I am facing a very similar problem after integrating datasets that were …
Answer: NCBI protein to NCBI cDNA (Ensembl conversions would be great as well) in R
by
James W. MacDonald
64k
I don't know what you mean by 'cDNA value'. That could mean any number of things, I suppose, particularly if you don't know what cDNA is (p…
Comment: How can we use the organism database created by makeorgPackageFromNCBI to KEGG a
by
Guido Hooiveld
★ 3.8k
What did you try yourselves? Again, please show your code....!! For KEGG-based analysis you can make use of the convenience functions `enr…
Comment: Deleted:No significant MVPs with a BH adjusted P-value below 0.05
by
Basti
▴ 740
The image is blurred, but you need to follow ATpoint advice and restart the entire analysis using a clean environment.
Votes
A: DSS understanding delta option and posterior probability
Comment: Ensembl down???
Answer: How should I run ssGSEA Hallmark Enrichment Analysis?
Answer: tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
Comment: Problem loading HDF5Array in R 4.3.2
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