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Showing :
PHYLOSEQ
•
reset
5
votes
11
replies
3.2k
views
Error while installing Phyloseq using biocLite
bioclite
phyloseq
install error
6.5 years ago
khp
▴ 30
4
votes
3
replies
1.5k
views
Paired-test between two groups within a condition after phyloseq_to_deseq2
DESeq2
phyloseq
updated 4.1 years ago by
Michael Love
43k • written 4.1 years ago by
trichorico
▴ 10
3
votes
2
replies
4.0k
views
DESeq2 iterative size factor normalization did not converge
deseq2
microbiome
phyloseq
updated 7.6 years ago by
Michael Love
43k • written 7.6 years ago by
couchc
• 0
3
votes
2
replies
2.4k
views
DESEQ2 (R) design/contrast formula questions
deseq2
phyloseq
multiple factor design
paired samples
updated 9.0 years ago by
mcmurdie
▴ 20 • written 9.0 years ago by
pete_bioinfo
▴ 10
2
votes
1
reply
2.1k
views
Using DESeq2 after agglomerating OTUs
phyloseq
deseq2
estimatesizefactors
updated 9.3 years ago by
Michael Love
43k • written 9.3 years ago by
brandilyn.peters
• 0
2
votes
9
replies
21k
views
Error in file(con, “r”) : cannot open the connection
r
phyloseq
import_biom
otu
qiime
updated 9.5 years ago by
mcmurdie
▴ 20 • written 9.5 years ago by
moanam
• 0
2
votes
2
replies
2.3k
views
Bioconductor phyloseq taking forever to install?
Bioconductor
phyloseq
4.4 years ago
garfield320
▴ 30
2
votes
2
replies
7.0k
views
Interpretation of intercept-only model (~1) in DESeq2
deseq2
phyloseq
updated 9.1 years ago by
Michael Love
43k • written 9.1 years ago by
piensaglobalmente
▴ 10
2
votes
1
reply
1.9k
views
Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq
microbiome
Software
updated 18 months ago by
ATpoint
★ 4.8k • written 18 months ago by
HULFRED
▴ 10
2
votes
1
reply
4.7k
views
does anyone how to create rarefaction curves from a phyloseq object?
phyloseq
Phylogenetics
updated 2.0 years ago by
RMiller
▴ 20 • written 2.0 years ago by
kevin
• 0
2
votes
2
replies
1.7k
views
DESeq2 in phyloseq
deseq2
phyloseq
8.1 years ago
sarahmacdonald86
• 0
1
vote
2
replies
2.9k
views
Bioconductor install error
phyloseq
Bioconductor
4.3 years ago
Tess
• 0
1
vote
1
reply
1.7k
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2
R
microbiome
phyloseq
qiime
updated 7.3 years ago by
Michael Love
43k • written 7.3 years ago by
ssingh59
• 0
1
vote
3
replies
1.4k
views
How to assign random effect factor in DESeq2 desing?
StatisticalMethod
DESeq2
phyloseq
updated 4.1 years ago by
Michael Love
43k • written 4.1 years ago by
zardbid
• 0
1
vote
2
replies
2.3k
views
DESeqs two-factor two-level, interaction is interested
Sequencing
GO
phyloseq
DESeq2
Sequencing
GO
phyloseq
DESeq2
updated 10.8 years ago by
Michael Love
43k • written 10.8 years ago by
Shucong Li
▴ 60
1
vote
1
reply
4.7k
views
Setting up bioconductor on a Linux server using conda
dada2
conda
phyloseq
updated 4.0 years ago by
James W. MacDonald
68k • written 4.0 years ago by
Daniel
• 0
1
vote
10
replies
2.5k
views
Multi-factor Comparison in DESeq 2 Issue
deseq2
phyloseq
updated 10.1 years ago by
Ryan C. Thompson
★ 7.9k • written 10.1 years ago by
locon833
• 0
1
vote
3
replies
2.3k
views
Error bars on DESeq2 visuals
deseq2
metagenomics
phyloseq
ggplot2
7.6 years ago
lauren.czaplicki
• 0
1
vote
2
replies
1.7k
views
rlogTransformation vs getVarianceStabilizedData
deseq2
r
phyloseq
updated 8.3 years ago by
Michael Love
43k • written 8.3 years ago by
fabian.roger08
▴ 10
1
vote
8
replies
6.9k
views
Cannot read Biom file
r
biomformat
phyloseq
updated 7.4 years ago by
Axel Klenk
★ 1.1k • written 7.4 years ago by
channen1221
• 0
1
vote
1
reply
4.1k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome
normalization
variancestabilizingtransformation
phyloseq
8.0 years ago
stats134711
• 0
0
votes
1
reply
2.0k
views
tip_glom and annotations?
ggtree
treeio
phyloseq
annotation
tip_glom
updated 7.1 years ago by
Guangchuang Yu
★ 1.2k • written 7.1 years ago by
werdnus
• 0
0
votes
1
reply
2.1k
views
Install package phyloseq
installation
phyloseq
updated 7.0 years ago by
Martin Morgan
25k • written 7.0 years ago by
layeb
• 0
0
votes
1
reply
1.1k
views
Invalid class DESeqDataSet object with Phyloseq
deseq2
phyloseq
updated 6.6 years ago by
Michael Love
43k • written 6.6 years ago by
amgodogma
▴ 10
0
votes
9
replies
2.9k
views
DESEQ2 / Phyloseq contrasts no longer work as before following update
deseq2
phyloseq
6.5 years ago
eoin
• 0
0
votes
1
reply
1.9k
views
Import_biom with tree problem
phyloseq
mothur
16s
6.4 years ago
andrebolerbarros
▴ 20
0
votes
2
replies
1.3k
views
Phyloseq to DESeq2
deseq2
phyloseq
updated 6.2 years ago by
Michael Love
43k • written 6.2 years ago by
staffordvigors
• 0
0
votes
0
replies
1.1k
views
Problems with creating phyloseq bar plots from a table with species data
phyloseq
microbiome analysis
6.1 years ago
lm795
▴ 10
0
votes
2
replies
3.4k
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 5.3 years ago by
Martin Morgan
25k • written 5.3 years ago by
crgarcia
• 0
0
votes
3
replies
1.4k
views
Nested design- phyloseq_to_deseq
deseq2
Phyloseq
Nested
updated 5.0 years ago by
Michael Love
43k • written 5.0 years ago by
mpuli011
• 0
0
votes
2
replies
2.4k
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
4.7 years ago
jaiber.solano.i
• 0
0
votes
1
reply
1.5k
views
Can I use pseudocounts for differential abundance of OTUs?
metagenomics
deseq2
PHYLOSEQ
updated 4.7 years ago by
Michael Love
43k • written 4.7 years ago by
dc
• 0
0
votes
3
replies
1.4k
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 8 months ago by
Карина
• 0 • written 22 months ago by
abhisek001
• 0
0
votes
0
replies
1.4k
views
Co-occurrence Network Analysis between Algae and Bacteria
igraph
networkanalysis
Phylogenetics
phyloseq
4.2 years ago
Chantel
• 0
0
votes
1
reply
922
views
error installing phyloseq
phyloseq
updated 2.8 years ago by
shepherl
4.1k • written 2.8 years ago by
Ezra
• 0
0
votes
2
replies
565
views
Issue when attempting to use output from DECIPHER IDtaxa (pr2 V5) with dada2/phyloseq
DECIPHER
taxonomyassignment
phyloseq
dada2
Pr2V5
updated 8 days ago by
Daniel
• 0 • written 11 weeks ago by
Maggie
• 0
0
votes
0
replies
1.0k
views
Construct a phyloseq object directly from the dada2 outputs
phyloseq
dada2
3.6 years ago
Manijeh
• 0
0
votes
1
reply
2.8k
views
Import MetaPhlAn3 to Phyloseq
Metaphlan3
Metagenomics
phyloseq
updated 3.8 years ago by
Levi Waldron
★ 1.1k • written 3.8 years ago by
Saraswati
• 0
0
votes
4
replies
2.3k
views
Cannot install Phyloseq and dada2
GenomeInfoDbData
phyloseq
dada2
3.2 years ago
ymtan
• 0
0
votes
3
replies
2.4k
views
I cannot install "microbiome"
GenomeInfoDbData
microbiome
phyloseq
updated 2.6 years ago by
Marcel Ramos
700 • written 2.6 years ago by
kikiki
• 0
0
votes
1
reply
1.1k
views
Deseq workflow for phyloseq object and complicated data structure?
phyloseq
DESeq2
updated 3.2 years ago by
Michael Love
43k • written 3.2 years ago by
dschnitzler
• 0
0
votes
3
replies
1.2k
views
Controversial DESEQ2 results
phyloseq
DESeq2
updated 2.8 years ago by
Michael Love
43k • written 2.8 years ago by
Stephan
• 0
0
votes
3
replies
1.1k
views
Installing Packages repeatedly
phyloseq
updated 3.8 years ago by
Kevin Blighe
★ 4.0k • written 3.8 years ago by
klltnq
• 0
0
votes
1
reply
904
views
Purpose of seqtabNoC
phyloseq
updated 3.8 years ago by
Kevin Blighe
★ 4.0k • written 3.8 years ago by
klltnq
• 0
0
votes
0
replies
775
views
Code Issue
phyloseq
3.8 years ago
klltnq
• 0
0
votes
0
replies
949
views
Construct Phylogenetic Tree
phyloseq
3.8 years ago
klltnq
• 0
0
votes
5
replies
7.7k
views
Problems with installation of 'phyloseq
phyloseq
updated 3.6 years ago by
Kevin Blighe
★ 4.0k • written 3.7 years ago by
Ina
• 0
0
votes
0
replies
1.8k
views
How to pool phyloseq data?
phyloseq
r
updated 3.0 years ago by
Michael Love
43k • written 3.0 years ago by
strep
• 0
0
votes
3
replies
1.4k
views
DESeq2: difficulty with contrasts and main effects
DESeq2
phyloseq
contrasts
updated 3.6 years ago by
Kevin Blighe
★ 4.0k • written 3.6 years ago by
Mir
• 0
0
votes
6
replies
1.7k
views
convert default phylip to sequential phylip
phyloseq
Phylogenetics
updated 23 months ago by
yrkkhdesiserials
• 0 • written 3.6 years ago by
memy
• 0
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Comment: Package developing and interoperation with Bioconductor
by
shepherl
4.1k
Using an example with SummarizedExperiment would satisfy the requirement; however the package should take the object directly and not just…
Comment: Error in H5Dclose(h5dataset) when trying to read in kallisto h5 files
by
Sofia
• 0
1. I have tried to update the packages and R but to no avail. I keep getting either this error or : `Error in H5Fclose(file$H5Identifier) …
Comment: Validity of SingleR with very small bulk RNAseq reference
by
Rohit
• 0
Hi @nhaus So, what did you end up doing in such a scenario? I am facing a similar challenge
Comment: CpGs with genomic positions greater than the chromosome size in EPICv2?
by
Joshua Llano
• 0
Thank you for your reply James. I was worried that it was my mistake.
Comment: Annotation package for Manduca sexta
by
GA
▴ 10
Thank you!
Votes
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2?
Answer: Explannation for ROAST results
A: How DiffBind run PCA based on peak data?
Looking for equivalent EPIC chip v1 vs. v2 annotation variables
Properly constructing a hypergeometric test
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