Showing : 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
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 42k • written 3.3 years ago by ▴ 10
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 ▴ 20 • written 8.1 years ago by ▴ 10
3
votes
2
replies
3.3k
views
DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
updated 6.7 years ago by 42k • written 6.7 years ago by • 0
2
votes
2
replies
1.5k
views
DESeq2 in phyloseq
deseq2 phyloseq
7.2 years ago sarahmacdonald86 • 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 ▴ 20 • written 8.6 years ago by • 0
2
votes
2
replies
1.6k
views
Bioconductor phyloseq taking forever to install?
Bioconductor phyloseq
3.5 years ago garfield320 ▴ 30
2
votes
2
replies
6.3k
views
Interpretation of intercept-only model (~1) in DESeq2
deseq2 phyloseq
updated 8.2 years ago by 42k • written 8.2 years ago by ▴ 10
2
votes
1
reply
1.1k
views
Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq microbiome Software
updated 8 months ago by ★ 4.1k • written 8 months ago by ▴ 10
2
votes
1
reply
1.9k
views
Using DESeq2 after agglomerating OTUs
phyloseq deseq2 estimatesizefactors
updated 8.5 years ago by 42k • written 8.5 years ago by • 0
1
vote
8
replies
5.9k
views
Cannot read Biom file
r biomformat phyloseq
updated 6.5 years ago by ★ 1.0k • written 6.5 years ago by • 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
1
vote
2
replies
2.3k
views
Bioconductor install error
phyloseq Bioconductor
3.5 years ago Tess • 0
1
vote
1
reply
1.4k
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
updated 6.5 years ago by 42k • written 6.5 years ago by • 0
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 42k • written 3.2 years ago by • 0
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 65k • written 3.1 years ago by • 0
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 ▴ 10 • written 14 months ago by • 0
1
vote
3
replies
1.9k
views
Error bars on DESeq2 visuals
deseq2 metagenomics phyloseq ggplot2
6.8 years ago lauren.czaplicki • 0
1
vote
10
replies
2.3k
views
Multi-factor Comparison in DESeq 2 Issue
deseq2 phyloseq
updated 9.3 years ago by ★ 7.9k • written 9.3 years ago by • 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 42k • written 9.9 years ago by ▴ 60
1
vote
2
replies
1.5k
views
rlogTransformation vs getVarianceStabilizedData
deseq2 r phyloseq
updated 7.5 years ago by 42k • written 7.5 years ago by ▴ 10
0
votes
1
reply
1.6k
views
tip_glom and annotations?
ggtree treeio phyloseq annotation tip_glom
updated 6.3 years ago by ★ 1.2k • written 6.3 years ago by • 0
0
votes
1
reply
1.7k
views
Install package phyloseq
installation phyloseq
updated 6.2 years ago by 25k • written 6.2 years ago by • 0
0
votes
1
reply
849
views
Invalid class DESeqDataSet object with Phyloseq
deseq2 phyloseq
updated 5.8 years ago by 42k • written 5.8 years ago by ▴ 10
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
0
votes
1
reply
1.6k
views
Import_biom with tree problem
phyloseq mothur 16s
5.6 years ago andrebolerbarros ▴ 20
0
votes
2
replies
985
views
Phyloseq to DESeq2
deseq2 phyloseq
updated 5.3 years ago by 42k • written 5.3 years ago by • 0
0
votes
0
replies
833
views
Problems with creating phyloseq bar plots from a table with species data
phyloseq microbiome analysis
5.3 years ago lm795 ▴ 10
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 25k • written 4.4 years ago by • 0
0
votes
3
replies
1.0k
views
Nested design- phyloseq_to_deseq
deseq2 Phyloseq Nested
updated 4.1 years ago by 42k • written 4.1 years ago by • 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
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 42k • written 3.8 years ago by • 0
0
votes
2
replies
746
views
Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 1 day ago by • 0 • written 11 months ago by • 0
0
votes
0
replies
1.1k
views
Co-occurrence Network Analysis between Algae and Bacteria
igraph networkanalysis Phylogenetics phyloseq
3.4 years ago Chantel • 0
0
votes
1
reply
679
views
error installing phyloseq
phyloseq
updated 23 months ago by 3.9k • written 23 months ago by • 0
0
votes
0
replies
780
views
Construct a phyloseq object directly from the dada2 outputs
phyloseq dada2
2.7 years ago Manijeh • 0
0
votes
1
reply
2.2k
views
Import MetaPhlAn3 to Phyloseq
Metaphlan3 Metagenomics phyloseq
updated 2.9 years ago by ★ 1.1k • written 2.9 years ago by • 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
1.7k
views
I cannot install "microbiome"
GenomeInfoDbData microbiome phyloseq
updated 21 months ago by 690 • written 21 months ago by • 0
0
votes
1
reply
775
views
Deseq workflow for phyloseq object and complicated data structure?
phyloseq DESeq2
updated 2.3 years ago by 42k • written 2.3 years ago by • 0
0
votes
3
replies
902
views
Controversial DESEQ2 results
phyloseq DESeq2
updated 23 months ago by 42k • written 23 months ago by • 0
0
votes
3
replies
795
views
Installing Packages repeatedly
phyloseq
updated 2.9 years ago by ★ 3.9k • written 2.9 years ago by • 0
0
votes
1
reply
698
views
Purpose of seqtabNoC
phyloseq
updated 2.9 years ago by ★ 3.9k • written 2.9 years ago by • 0
0
votes
0
replies
627
views
Code Issue
phyloseq
2.9 years ago klltnq • 0
0
votes
0
replies
741
views
Construct Phylogenetic Tree
phyloseq
2.9 years ago klltnq • 0
0
votes
5
replies
6.4k
views
Problems with installation of 'phyloseq
phyloseq
updated 2.8 years ago by ★ 3.9k • written 2.8 years ago by • 0
0
votes
0
replies
1.4k
views
How to pool phyloseq data?
phyloseq r
updated 2.2 years ago by 42k • written 2.2 years ago by • 0
0
votes
3
replies
1.0k
views
DESeq2: difficulty with contrasts and main effects
DESeq2 phyloseq contrasts
updated 2.8 years ago by ★ 3.9k • written 2.8 years ago by • 0
0
votes
6
replies
1.4k
views
convert default phylip to sequential phylip
phyloseq Phylogenetics
updated 12 months ago by • 0 • written 2.7 years ago by • 0
0
votes
0
replies
507
views
Association between ohylum and genus on microbiome data sets.
phyloseq
2.0 years ago Edmond • 0
50 results • Page 1 of 1
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Replies
Comment: Ensembl plants at annotationHub? by Daniele • 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools by BioinfGuru ▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by makala • 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by Erik Wright ▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa by Matthew Thornton ▴ 360
So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!
Votes
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
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
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