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phyloseq
•
reset
2
votes
9
replies
20k
views
Error in file(con, “r”) : cannot open the connection
r
phyloseq
import_biom
otu
qiime
updated 8.6 years ago by
mcmurdie
▴ 20 • written 8.6 years ago by
moanam
• 0
0
votes
5
replies
6.5k
views
Problems with installation of 'phyloseq
phyloseq
updated 2.8 years ago by
Kevin Blighe
★ 3.9k • written 2.8 years ago by
Ina
• 0
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
42k • written 8.2 years ago by
piensaglobalmente
▴ 10
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
0
votes
1
reply
4.5k
views
Phyloseq: How to add sample table to phyloseq object
phyloseq
sample_table
phyloseq
9.3 years ago
Brian Smith
▴ 120
1
vote
1
reply
3.7k
views
Setting up bioconductor on a Linux server using conda
dada2
conda
phyloseq
updated 3.1 years ago by
James W. MacDonald
65k • written 3.2 years ago by
Daniel
• 0
1
vote
1
reply
3.5k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome
normalization
variancestabilizingtransformation
phyloseq
7.1 years ago
stats134711
• 0
3
votes
2
replies
3.4k
views
DESeq2 iterative size factor normalization did not converge
deseq2
microbiome
phyloseq
updated 6.7 years ago by
Michael Love
42k • written 6.7 years ago by
couchc
• 0
0
votes
6
replies
3.2k
views
Alpha diversity on Rlogtransformed data
deseq2
phyloseq
metagenomeseq
8.4 years ago
David
▴ 860
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
5
votes
11
replies
2.8k
views
Error while installing Phyloseq using biocLite
bioclite
phyloseq
install error
5.6 years ago
khp
▴ 30
1
vote
1
reply
2.6k
views
does anyone how to create rarefaction curves from a phyloseq object?
phyloseq
Phylogenetics
updated 14 months ago by
RMiller
▴ 10 • written 14 months ago by
kevin
• 0
0
votes
9
replies
2.4k
views
DESEQ2 / Phyloseq contrasts no longer work as before following update
deseq2
phyloseq
5.7 years ago
eoin
• 0
1
vote
2
replies
2.4k
views
Bioconductor install error
phyloseq
Bioconductor
3.5 years ago
Tess
• 0
1
vote
10
replies
2.3k
views
Multi-factor Comparison in DESeq 2 Issue
deseq2
phyloseq
updated 9.3 years ago by
Ryan C. Thompson
★ 7.9k • written 9.3 years ago by
locon833
• 0
0
votes
1
reply
2.2k
views
phyloseq merge_samples attempt to set rownames on an object with no dimensions
phyloseq
merge_samples
rownames
error
7.6 years ago
newmanss
• 0
0
votes
1
reply
2.2k
views
Import MetaPhlAn3 to Phyloseq
Metaphlan3
Metagenomics
phyloseq
updated 2.9 years ago by
Levi Waldron
★ 1.1k • written 2.9 years ago by
Saraswati
• 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 9.9 years ago by
Michael Love
42k • written 9.9 years ago by
Shucong Li
▴ 60
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 8.2 years ago by
pete_bioinfo
▴ 10
0
votes
1
reply
2.1k
views
ggtree facet_plot question using geom_boxplot to plot abundance data corresponding to tree tips
ggtree
ggplot2
phyloseq
geom_boxplot
facet_plot
updated 7.2 years ago by
Guangchuang Yu
★ 1.2k • written 7.2 years ago by
matthew.wipperman
• 0
0
votes
1
reply
2.0k
views
Error with phyloseq R package with Conda install
software error
phyloseq
anaconda
written 7.5 years ago by
kpitz23
• 0
0
votes
3
replies
2.0k
views
Newer version of DESeq2 gives different results
deseq2
phyloseq
updated 7.9 years ago by
Michael Love
42k • written 7.9 years ago by
am39
• 0
0
votes
1
reply
2.0k
views
phyloseq biom json format conversion needed to hdf5 format for qiime
biom
json
hdf5
qiime
phyloseq
updated 7.6 years ago by
Bernd Fischer
▴ 550 • written 7.6 years ago by
newmanss
• 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
3.9 years ago
jaiber.solano.i
• 0
1
vote
3
replies
1.9k
views
Error bars on DESeq2 visuals
deseq2
metagenomics
phyloseq
ggplot2
6.8 years ago
lauren.czaplicki
• 0
0
votes
4
replies
1.9k
views
Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings
phyloseq
updated 2.2 years ago by
James W. MacDonald
65k • written 2.2 years ago by
Eman
• 0
2
votes
1
reply
1.9k
views
Using DESeq2 after agglomerating OTUs
phyloseq
deseq2
estimatesizefactors
updated 8.5 years ago by
Michael Love
42k • written 8.5 years ago by
brandilyn.peters
• 0
0
votes
2
replies
1.9k
views
Controlling colours assigned to order in DeSeq2 plot in phyloseq
phyloseq
color
ggplot2
updated 7.2 years ago by
Michael Love
42k • written 7.2 years ago by
sarahmacdonald86
• 0
0
votes
4
replies
1.8k
views
Cannot install Phyloseq and dada2
GenomeInfoDbData
phyloseq
dada2
2.3 years ago
ymtan
• 0
0
votes
1
reply
1.7k
views
Install package phyloseq
installation
phyloseq
updated 6.2 years ago by
Martin Morgan
25k • written 6.2 years ago by
layeb
• 0
0
votes
3
replies
1.7k
views
I cannot install "microbiome"
GenomeInfoDbData
microbiome
phyloseq
updated 21 months ago by
Marcel Ramos
700 • written 21 months ago by
kikiki
• 0
2
votes
2
replies
1.6k
views
Bioconductor phyloseq taking forever to install?
Bioconductor
phyloseq
3.6 years ago
garfield320
▴ 30
0
votes
1
reply
1.6k
views
tip_glom and annotations?
ggtree
treeio
phyloseq
annotation
tip_glom
updated 6.3 years ago by
Guangchuang Yu
★ 1.2k • written 6.3 years ago by
werdnus
• 0
0
votes
3
replies
1.6k
views
DESeq2 blocking by condition over time
deseq2
phyloseq
time course
7.7 years ago
akp
• 0
0
votes
1
reply
1.6k
views
Import_biom with tree problem
phyloseq
mothur
16s
5.6 years ago
andrebolerbarros
▴ 20
0
votes
1
reply
1.5k
views
Phyloseq to DESeq2 with multiple variables
deseq2
phyloseq
multiple time points
updated 6.8 years ago by
Michael Love
42k • written 6.8 years ago by
campbell87
• 0
0
votes
0
replies
1.5k
views
Loading Phyloseq into R- R crashes
software error
phyloseq
R
9.4 years ago
locon833
• 0
2
votes
2
replies
1.5k
views
DESeq2 in phyloseq
deseq2
phyloseq
7.2 years ago
sarahmacdonald86
• 0
1
vote
2
replies
1.5k
views
rlogTransformation vs getVarianceStabilizedData
deseq2
r
phyloseq
updated 7.5 years ago by
Michael Love
42k • written 7.5 years ago by
fabian.roger08
▴ 10
1
vote
1
reply
1.4k
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2
R
microbiome
phyloseq
qiime
updated 6.5 years ago by
Michael Love
42k • written 6.5 years ago by
ssingh59
• 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
1.4k
views
How to pool phyloseq data?
phyloseq
r
updated 2.2 years ago by
Michael Love
42k • written 2.2 years ago by
strep
• 0
0
votes
1
reply
1.3k
views
phyloseq - plot_bar() error
phyloseq
plot_bar()
updated 8.5 years ago by
mcmurdie
▴ 20 • written 8.5 years ago by
Brian Smith
▴ 120
0
votes
1
reply
1.3k
views
phyloseq heatmap blank after multiple package updates
phyloseq
heatmap
updated 6.7 years ago by
Wolfgang Huber
★ 13k • written 6.7 years ago by
newmanss
• 0
0
votes
0
replies
1.3k
views
Phylogenetic tree from marker genes
ape
phyloseq
dist
metagenomics
7.1 years ago
David
▴ 860
0
votes
1
reply
1.3k
views
DESeqs two-factor two-level, interaction is interested
Sequencing
GO
phyloseq
DESeq2
Sequencing
GO
phyloseq
DESeq2
9.9 years ago
Shucong Li
▴ 60
0
votes
0
replies
1.3k
views
Problem with ade4 when upgrading to Rstudio 1.1 and OpenR 3.4
phyloseq
installation
ade4
macos
6.6 years ago
sprague
• 0
0
votes
0
replies
1.2k
views
Phyloseq/DEseq transformed data
DESeq
phyloseq
DESeq
phyloseq
10.1 years ago
Susan Holmes
▴ 120
4
votes
3
replies
1.2k
views
Paired-test between two groups within a condition after phyloseq_to_deseq2
DESeq2
phyloseq
updated 3.3 years ago by
Michael Love
42k • written 3.3 years ago by
trichorico
▴ 10
0
votes
1
reply
1.1k
views
Can I use pseudocounts for differential abundance of OTUs?
metagenomics
deseq2
PHYLOSEQ
updated 3.8 years ago by
Michael Love
42k • written 3.8 years ago by
dc
• 0
50 results • Page
1 of 1
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Replies
Answer: all variables in design formula must be columns in colData (Deseq2) error
by
ATpoint
★ 4.1k
Your code is poorly readable. Suggest you select and then highlight with markdown using the `10101` button. Generally, colData(dds) must…
Answer: Subsetting RNAseq data | voomaByGroup()
by
Gordon Smyth
50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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