Showing : PHYLOSEQ • reset
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Co-occurrence Network Analysis between Algae and Bacteria
igraph networkanalysis Phylogenetics phyloseq
updated 1 day ago by ▴ 40 • written 4.9 years ago by • 0
1
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3
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1.7k
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How can I correctly use phyloseq with Docker?
phylo phyloseq Docker
written 6 months ago by • 0
0
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1
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407
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DESeq2 from phyloseq error
DESeq2 phyloseq
6 months ago asafpr • 0
0
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2
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891
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Issue when attempting to use output from DECIPHER IDtaxa (pr2 V5) with dada2/phyloseq
DECIPHER taxonomyassignment phyloseq dada2 Pr2V5
updated 8 months ago by • 0 • written 10 months ago by • 0
0
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3
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1.8k
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Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 16 months ago by • 0 • written 2.5 years ago by • 0
2
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1
reply
2.3k
views
Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq microbiome Software
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by ▴ 10
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894
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Try to understand better how to set out an effective sample size within the MetagenomSeq package in microbiome ?
Metagenomics metagenomeSeq microbiome phyloseq microbiomeDataSets
2.3 years ago Mohamed ▴ 30
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6
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1.9k
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convert default phylip to sequential phylip
phyloseq Phylogenetics
updated 2.6 years ago by • 0 • written 4.2 years ago by • 0
2
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1
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5.5k
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does anyone how to create rarefaction curves from a phyloseq object?
phyloseq Phylogenetics
updated 2.7 years ago by ▴ 20 • written 2.7 years ago by • 0
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3
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2.7k
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I cannot install "microbiome"
GenomeInfoDbData microbiome phyloseq
updated 3.3 years ago by 700 • written 3.3 years ago by • 0
0
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1
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1.1k
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error installing phyloseq
phyloseq
updated 3.4 years ago by 4.2k • written 3.4 years ago by • 0
0
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3
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1.4k
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Controversial DESEQ2 results
phyloseq DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
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852
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Association between ohylum and genus on microbiome data sets.
phyloseq
3.5 years ago Edmond • 0
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0
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2.0k
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How to pool phyloseq data?
phyloseq r
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
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4
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3.0k
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Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings phyloseq
updated 3.7 years ago by 68k • written 3.7 years ago by • 0
0
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1
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1.3k
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Deseq workflow for phyloseq object and complicated data structure?
phyloseq DESeq2
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
0
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4
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2.7k
views
Cannot install Phyloseq and dada2
GenomeInfoDbData phyloseq dada2
3.8 years ago ymtan • 0
0
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1
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1.1k
views
Error in 'differential_abundance'
phyloseq devtools
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
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0
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1.3k
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Construct a phyloseq object directly from the dada2 outputs
phyloseq dada2
4.3 years ago Manijeh • 0
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3
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1.6k
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DESeq2: difficulty with contrasts and main effects
DESeq2 phyloseq contrasts
updated 4.3 years ago by ★ 4.0k • written 4.3 years ago by • 0
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5
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8.3k
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Problems with installation of 'phyloseq
phyloseq
updated 4.3 years ago by ★ 4.0k • written 4.3 years ago by • 0
0
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1
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1.1k
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Purpose of seqtabNoC
phyloseq
updated 4.4 years ago by ★ 4.0k • written 4.4 years ago by • 0
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0
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1.1k
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Construct Phylogenetic Tree
phyloseq
4.4 years ago klltnq • 0
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0
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881
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Code Issue
phyloseq
4.4 years ago klltnq • 0
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3
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1.2k
views
Installing Packages repeatedly
phyloseq
updated 4.4 years ago by ★ 4.0k • written 4.4 years ago by • 0
0
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1
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3.1k
views
Import MetaPhlAn3 to Phyloseq
Metaphlan3 Metagenomics phyloseq
updated 4.4 years ago by ★ 1.1k • written 4.4 years ago by • 0
1
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1
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5.5k
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Setting up bioconductor on a Linux server using conda
dada2 conda phyloseq
updated 4.7 years ago by 68k • written 4.7 years ago by • 0
1
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3
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1.7k
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How to assign random effect factor in DESeq2 desing?
StatisticalMethod DESeq2 phyloseq
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
4
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3
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1.6k
views
Paired-test between two groups within a condition after phyloseq_to_deseq2
DESeq2 phyloseq
updated 4.8 years ago by 43k • written 4.8 years ago by ▴ 10
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2
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3.2k
views
Bioconductor install error
phyloseq Bioconductor
5.0 years ago Tess • 0
2
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2
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2.7k
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Bioconductor phyloseq taking forever to install?
Bioconductor phyloseq
5.1 years ago garfield320 ▴ 30
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1.7k
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Can I use pseudocounts for differential abundance of OTUs?
metagenomics deseq2 PHYLOSEQ
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
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2.7k
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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
5.4 years ago jaiber.solano.i • 0
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3
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1.5k
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Nested design- phyloseq_to_deseq
deseq2 Phyloseq Nested
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
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2
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3.7k
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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 5.9 years ago by 25k • written 5.9 years ago by • 0
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1.3k
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Problems with creating phyloseq bar plots from a table with species data
phyloseq microbiome analysis
6.8 years ago lm795 ▴ 10
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2
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1.5k
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Phyloseq to DESeq2
deseq2 phyloseq
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
0
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1
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2.1k
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Import_biom with tree problem
phyloseq mothur 16s
7.1 years ago andrebolerbarros ▴ 20
5
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11
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3.5k
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Error while installing Phyloseq using biocLite
bioclite phyloseq install error
7.1 years ago khp ▴ 30
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9
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3.2k
views
DESEQ2 / Phyloseq contrasts no longer work as before following update
deseq2 phyloseq
7.2 years ago eoin • 0
0
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1
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1.4k
views
Invalid class DESeqDataSet object with Phyloseq
deseq2 phyloseq
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 10
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1
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2.4k
views
Install package phyloseq
installation phyloseq
updated 7.7 years ago by 25k • written 7.7 years ago by • 0
0
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1
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2.2k
views
tip_glom and annotations?
ggtree treeio phyloseq annotation tip_glom
updated 7.8 years ago by ★ 1.2k • written 7.8 years ago by • 0
1
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1
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1.8k
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Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
1
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8
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7.3k
views
Cannot read Biom file
r biomformat phyloseq
updated 8.1 years ago by ★ 1.1k • written 8.1 years ago by • 0
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0
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1.8k
views
Problem with ade4 when upgrading to Rstudio 1.1 and OpenR 3.4
phyloseq installation ade4 macos
8.1 years ago sprague • 0
3
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2
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4.3k
views
DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
updated 8.2 years ago by 43k • written 8.2 years ago by • 0
0
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1
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1.9k
views
phyloseq heatmap blank after multiple package updates
phyloseq heatmap
updated 8.2 years ago by ★ 13k • written 8.2 years ago by • 0
1
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3
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2.6k
views
Error bars on DESeq2 visuals
deseq2 metagenomics phyloseq ggplot2
8.3 years ago lauren.czaplicki • 0
0
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1
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2.1k
views
Phyloseq to DESeq2 with multiple variables
deseq2 phyloseq multiple time points
updated 8.4 years ago by 43k • written 8.4 years ago by • 0
76 results • Page 1 of 2
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Replies
Comment: Post translational modifications and phosphoproteomics in limpa? by james.eapen • 0
Thank you!
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by ATpoint ★ 5.0k
The donor effect is crystal clear, and absent in these suspicious samples. It strongly argues for a technical problem. If you really need s…
Answer: mzR-Rcpp compiler version issue by Laurent Gatto 1.6k
There are two issues here. First, a warning about mzR, that you can safely ignore. It tells you that mzR was compiled using a different …
Comment: Identifying differentially expressed genes in individual samples from a large co by jamie.gearing ▴ 60
Great. Yes, something descriptive is probably good enough, even if the p-values themselves are not so rigorous. Thanks very much Gordon!
Comment: Co-occurrence Network Analysis between Algae and Bacteria by Stefano Mangiola ▴ 40
Just a placeholder, that we are extending `sccomp` to co-occurrence analyses. Yours could be a good use-case to test first. We will be in t…
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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