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PHYLOSEQ
•
reset
0
votes
0
replies
1.7k
views
Phylogenetic tree from marker genes
ape
phyloseq
dist
metagenomics
8.6 years ago
David
▴ 860
1
vote
1
reply
4.4k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome
normalization
variancestabilizingtransformation
phyloseq
8.6 years ago
stats134711
• 0
0
votes
1
reply
2.6k
views
ggtree facet_plot question using geom_boxplot to plot abundance data corresponding to tree tips
ggtree
ggplot2
phyloseq
geom_boxplot
facet_plot
updated 8.7 years ago by
Guangchuang Yu
★ 1.2k • written 8.7 years ago by
matthew.wipperman
• 0
2
votes
2
replies
1.9k
views
DESeq2 in phyloseq
deseq2
phyloseq
8.7 years ago
sarahmacdonald86
• 0
0
votes
2
replies
2.4k
views
Controlling colours assigned to order in DeSeq2 plot in phyloseq
phyloseq
color
ggplot2
updated 8.7 years ago by
Michael Love
43k • written 8.7 years ago by
sarahmacdonald86
• 0
1
vote
2
replies
1.8k
views
rlogTransformation vs getVarianceStabilizedData
deseq2
r
phyloseq
updated 9.0 years ago by
Michael Love
43k • written 9.0 years ago by
fabian.roger08
▴ 10
0
votes
1
reply
2.6k
views
Error with phyloseq R package with Conda install
software error
phyloseq
anaconda
written 9.0 years ago by
kpitz23
• 0
0
votes
1
reply
2.5k
views
phyloseq biom json format conversion needed to hdf5 format for qiime
biom
json
hdf5
qiime
phyloseq
updated 9.1 years ago by
Bernd Fischer
▴ 550 • written 9.1 years ago by
newmanss
• 0
0
votes
1
reply
2.7k
views
phyloseq merge_samples attempt to set rownames on an object with no dimensions
phyloseq
merge_samples
rownames
error
9.2 years ago
newmanss
• 0
0
votes
3
replies
1.9k
views
DESeq2 blocking by condition over time
deseq2
phyloseq
time course
9.2 years ago
akp
• 0
0
votes
0
replies
1.0k
views
displaying network from microbial count data
phyloseq
9.3 years ago
chrisclarkson100
▴ 50
0
votes
0
replies
1.1k
views
Testing for OTUs with negatively correlated abundances/occurrences
phyloseq
9.3 years ago
am39
• 0
0
votes
3
replies
2.4k
views
Newer version of DESeq2 gives different results
deseq2
phyloseq
updated 9.5 years ago by
Michael Love
43k • written 9.5 years ago by
am39
• 0
0
votes
1
reply
1.3k
views
Aditional undesired sample
phyloseq
9.6 years ago
sanrrone
• 0
3
votes
2
replies
2.5k
views
DESEQ2 (R) design/contrast formula questions
deseq2
phyloseq
multiple factor design
paired samples
updated 9.6 years ago by
mcmurdie
▴ 20 • written 9.7 years ago by
pete_bioinfo
▴ 10
2
votes
2
replies
7.3k
views
Interpretation of intercept-only model (~1) in DESeq2
deseq2
phyloseq
updated 9.7 years ago by
Michael Love
43k • written 9.7 years ago by
piensaglobalmente
▴ 10
0
votes
6
replies
4.0k
views
Alpha diversity on Rlogtransformed data
deseq2
phyloseq
metagenomeseq
10.0 years ago • updated 9.9 years ago
David
▴ 860
2
votes
1
reply
2.2k
views
Using DESeq2 after agglomerating OTUs
phyloseq
deseq2
estimatesizefactors
updated 10.0 years ago by
Michael Love
43k • written 10.0 years ago by
brandilyn.peters
• 0
0
votes
1
reply
1.7k
views
phyloseq - plot_bar() error
phyloseq
plot_bar()
updated 10.0 years ago by
mcmurdie
▴ 20 • written 10.0 years ago by
Brian Smith
▴ 120
2
votes
9
replies
21k
views
Error in file(con, “r”) : cannot open the connection
r
phyloseq
import_biom
otu
qiime
updated 10.1 years ago by
mcmurdie
▴ 20 • written 10.1 years ago by
moanam
• 0
1
vote
10
replies
2.8k
views
Multi-factor Comparison in DESeq 2 Issue
deseq2
phyloseq
updated 10.8 years ago by
Ryan C. Thompson
★ 7.9k • written 10.8 years ago by
locon833
• 0
0
votes
3
replies
5.7k
views
Phyloseq: How to add sample table to phyloseq object
phyloseq
sample_table
phyloseq
written 10.8 years ago by
Brian Smith
▴ 120
0
votes
0
replies
1.8k
views
Loading Phyloseq into R- R crashes
software error
phyloseq
R
10.9 years ago
locon833
• 0
0
votes
1
reply
1.7k
views
DESeqs two-factor two-level, interaction is interested
Sequencing
GO
phyloseq
DESeq2
Sequencing
GO
phyloseq
DESeq2
11.4 years ago
Shucong Li
▴ 60
1
vote
2
replies
2.4k
views
DESeqs two-factor two-level, interaction is interested
Sequencing
GO
phyloseq
DESeq2
Sequencing
GO
phyloseq
DESeq2
updated 11.4 years ago by
Michael Love
43k • written 11.4 years ago by
Shucong Li
▴ 60
0
votes
0
replies
1.4k
views
Phyloseq/DEseq transformed data
DESeq
phyloseq
DESeq
phyloseq
11.6 years ago
Susan Holmes
▴ 120
76 results • Page
2 of 2
Recent ...
Replies
Answer: Create consensusMatrix for codon bases
by
Kevin Blighe
★ 4.0k
To address your query on generating a codon frequency matrix analogous to the output from `consensusMatrix` for a `DNAStringSet` object, no…
Answer: Finding duplicated entries in GRangesList
by
Kevin Blighe
★ 4.0k
The duplicated and unique functions operate element-wise on GRangesList objects. This means that they apply the respective function to each…
Answer: sigDF object in sesame
by
Kevin Blighe
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Your interpretation of the column headers in the SigDF object is correct: MG corresponds to the methylated signal intensity in the green ch…
Answer: DESeq2 on non-RNASeq counts data
by
Kevin Blighe
★ 4.0k
The use of DESeq2 for count data from artificial sequences is acceptable, as the program models counts via a negative binomial distribution…
Answer: After running samtools, the featureCounts command crashed.
by
Kevin Blighe
★ 4.0k
Hello Rui Tang, The buffer overflow error in featureCounts that you encountered is likely due to a compatibility issue between the Subre…
Votes
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Identifying differentially expressed genes in individual samples from a large co
Answer: Identifying differentially expressed genes in individual samples from a large co
Bioconductor Seminar Series - Dec 2: Deep-learning Gene Perturbation Effect Prediction
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