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PHYLOSEQ
•
reset
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
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
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
9
replies
2.4k
views
DESEQ2 / Phyloseq contrasts no longer work as before following update
deseq2
phyloseq
5.6 years ago
eoin
• 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
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
6
replies
3.2k
views
Alpha diversity on Rlogtransformed data
deseq2
phyloseq
metagenomeseq
8.4 years ago
David
▴ 860
0
votes
5
replies
6.4k
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
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 2.1 years ago by
James W. MacDonald
65k • written 2.2 years ago by
Eman
• 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
DESeq2 blocking by condition over time
deseq2
phyloseq
time course
7.7 years ago
akp
• 0
0
votes
3
replies
1.6k
views
I cannot install "microbiome"
GenomeInfoDbData
microbiome
phyloseq
updated 21 months ago by
Marcel Ramos
690 • written 21 months ago by
kikiki
• 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
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
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
0
votes
3
replies
1.0k
views
DESeq2: difficulty with contrasts and main effects
DESeq2
phyloseq
contrasts
updated 2.8 years ago by
Kevin Blighe
★ 3.9k • written 2.8 years ago by
Mir
• 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
41k • written 7.9 years ago by
am39
• 0
0
votes
3
replies
778
views
Installing Packages repeatedly
phyloseq
updated 2.9 years ago by
Kevin Blighe
★ 3.9k • written 2.9 years ago by
klltnq
• 0
1
vote
3
replies
1.9k
views
Error bars on DESeq2 visuals
deseq2
metagenomics
phyloseq
ggplot2
6.7 years ago
lauren.czaplicki
• 0
0
votes
3
replies
889
views
Controversial DESEQ2 results
phyloseq
DESeq2
updated 23 months ago by
Michael Love
41k • written 23 months ago by
Stephan
• 0
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
2
replies
1.8k
views
Controlling colours assigned to order in DeSeq2 plot in phyloseq
phyloseq
color
ggplot2
updated 7.2 years ago by
Michael Love
41k • written 7.2 years ago by
sarahmacdonald86
• 0
2
votes
2
replies
1.5k
views
DESeq2 in phyloseq
deseq2
phyloseq
7.2 years ago
sarahmacdonald86
• 0
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
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
2
votes
2
replies
1.6k
views
Bioconductor phyloseq taking forever to install?
Bioconductor
phyloseq
3.5 years ago
garfield320
▴ 30
1
vote
2
replies
2.3k
views
Bioconductor install error
phyloseq
Bioconductor
3.5 years ago
Tess
• 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
41k • written 9.9 years ago by
Shucong Li
▴ 60
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
3
votes
2
replies
3.3k
views
DESeq2 iterative size factor normalization did not converge
deseq2
microbiome
phyloseq
updated 6.7 years ago by
Michael Love
41k • written 6.7 years ago by
couchc
• 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
41k • written 8.2 years ago by
piensaglobalmente
▴ 10
0
votes
2
replies
978
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
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
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 • updated 9.8 years ago
Shucong Li
▴ 60
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
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
987
views
Aditional undesired sample
phyloseq
8.1 years ago
sanrrone
• 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
1.9k
views
phyloseq biom json format conversion needed to hdf5 format for qiime
biom
json
hdf5
qiime
phyloseq
updated 7.5 years ago by
Bernd Fischer
▴ 550 • written 7.5 years ago by
newmanss
• 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
1
reply
2.0k
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
1
vote
1
reply
3.5k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome
normalization
variancestabilizingtransformation
phyloseq
7.1 years ago
stats134711
• 0
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
41k • written 6.8 years ago by
campbell87
• 0
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
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
0
votes
1
reply
1.6k
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
840
views
Invalid class DESeqDataSet object with Phyloseq
deseq2
phyloseq
updated 5.8 years ago by
Michael Love
41k • written 5.8 years ago by
amgodogma
▴ 10
0
votes
1
reply
1.5k
views
Import_biom with tree problem
phyloseq
mothur
16s
5.5 years ago
andrebolerbarros
▴ 20
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
41k • written 3.8 years ago by
dc
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea()
by
James W. MacDonald
65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea()
by
Chris
• 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Comment: Help with running egsea()
by
James W. MacDonald
65k
I don't understand the last question, but do look at the msigdb.gsets argument to `buildIdx` in the help page for that function.
Votes
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
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