Showing : Phyloseq • reset
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Co-occurrence Network Analysis between Algae and Bacteria
igraph networkanalysis Phylogenetics phyloseq
written 4.8 years ago by • 0
1
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3
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1.6k
views
How can I correctly use phyloseq with Docker?
phylo phyloseq Docker
written 6 months ago by • 0
0
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1
reply
384
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DESeq2 from phyloseq error
DESeq2 phyloseq
5 months ago asafpr • 0
0
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2
replies
862
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Issue when attempting to use output from DECIPHER IDtaxa (pr2 V5) with dada2/phyloseq
DECIPHER taxonomyassignment phyloseq dada2 Pr2V5
updated 7 months ago by • 0 • written 9 months ago by • 0
0
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3
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1.7k
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Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 15 months ago by • 0 • written 2.4 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 2.1 years ago by ★ 5.0k • written 2.1 years ago by ▴ 10
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837
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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
2.2 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 2.5 years ago by • 0 • written 4.2 years ago by • 0
2
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1
reply
5.4k
views
does anyone how to create rarefaction curves from a phyloseq object?
phyloseq Phylogenetics
updated 2.6 years ago by ▴ 20 • written 2.6 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 3.2 years ago by 700 • written 3.2 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
views
Controversial DESEQ2 results
phyloseq DESeq2
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
0
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0
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838
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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 3.6 years ago by 43k • written 3.6 years ago by • 0
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 3.6 years ago by 68k • written 3.6 years ago by • 0
0
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1
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1.2k
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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
replies
2.6k
views
Cannot install Phyloseq and dada2
GenomeInfoDbData phyloseq dada2
3.8 years ago ymtan • 0
0
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1
reply
1.1k
views
Error in 'differential_abundance'
phyloseq devtools
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
0
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0
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1.2k
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Construct a phyloseq object directly from the dada2 outputs
phyloseq dada2
4.2 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 4.2 years ago by ★ 4.0k • written 4.2 years ago by • 0
0
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5
replies
8.2k
views
Problems with installation of 'phyloseq
phyloseq
updated 4.2 years ago by ★ 4.0k • written 4.2 years ago by • 0
0
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1
reply
1.0k
views
Purpose of seqtabNoC
phyloseq
updated 4.3 years ago by ★ 4.0k • written 4.3 years ago by • 0
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0
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1.1k
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Construct Phylogenetic Tree
phyloseq
4.3 years ago klltnq • 0
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0
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863
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Code Issue
phyloseq
4.3 years ago klltnq • 0
0
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3
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1.2k
views
Installing Packages repeatedly
phyloseq
updated 4.3 years ago by ★ 4.0k • written 4.3 years ago by • 0
0
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1
reply
3.0k
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
reply
5.4k
views
Setting up bioconductor on a Linux server using conda
dada2 conda phyloseq
updated 4.6 years ago by 68k • written 4.6 years ago by • 0
1
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3
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1.6k
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How to assign random effect factor in DESeq2 desing?
StatisticalMethod DESeq2 phyloseq
updated 4.7 years ago by 43k • written 4.7 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 4.7 years ago by 43k • written 4.7 years ago by ▴ 10
1
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2
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3.2k
views
Bioconductor install error
phyloseq Bioconductor
4.9 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
5.0 years ago garfield320 ▴ 30
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1
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1.7k
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Can I use pseudocounts for differential abundance of OTUs?
metagenomics deseq2 PHYLOSEQ
updated 5.2 years ago by 43k • written 5.3 years ago by • 0
0
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2
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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
5.3 years ago jaiber.solano.i • 0
0
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3
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1.5k
views
Nested design- phyloseq_to_deseq
deseq2 Phyloseq Nested
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
0
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2
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3.6k
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 5.9 years ago by 25k • written 5.9 years ago by • 0
0
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0
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1.2k
views
Problems with creating phyloseq bar plots from a table with species data
phyloseq microbiome analysis
6.7 years ago lm795 ▴ 10
0
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2
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1.4k
views
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
reply
2.0k
views
Import_biom with tree problem
phyloseq mothur 16s
7.0 years ago andrebolerbarros ▴ 20
5
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11
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3.5k
views
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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3.1k
views
DESEQ2 / Phyloseq contrasts no longer work as before following update
deseq2 phyloseq
7.1 years ago eoin • 0
0
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1
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1.3k
views
Invalid class DESeqDataSet object with Phyloseq
deseq2 phyloseq
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 10
0
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1
reply
2.4k
views
Install package phyloseq
installation phyloseq
updated 7.6 years ago by 25k • written 7.6 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 7.7 years ago by ★ 1.2k • written 7.7 years ago by • 0
1
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1
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1.8k
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
1
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8
replies
7.3k
views
Cannot read Biom file
r biomformat phyloseq
updated 8.0 years ago by ★ 1.1k • written 8.0 years ago by • 0
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
8.0 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 8.1 years ago by 43k • written 8.1 years ago by • 0
0
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1
reply
1.8k
views
phyloseq heatmap blank after multiple package updates
phyloseq heatmap
updated 8.1 years ago by ★ 13k • written 8.2 years ago by • 0
1
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3
replies
2.5k
views
Error bars on DESeq2 visuals
deseq2 metagenomics phyloseq ggplot2
8.2 years ago lauren.czaplicki • 0
0
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1
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2.0k
views
Phyloseq to DESeq2 with multiple variables
deseq2 phyloseq multiple time points
updated 8.3 years ago by 43k • written 8.3 years ago by • 0
76 results • Page 1 of 2
Recent ...
Replies
Comment: deseq2 filter the low counts by empty_mt • 0
Hi Michael, My matrix consists of 36 samples from 6 treatments (6 samples/ treatment), whether I adjust prefiltering parameters or not, in…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
That works. I didn't realize what you said about HDF5 files. We always keep those and archive the MTX files. I'm able to read in the file…
Comment: DESeq2 interactions by Michael Love 43k
GPT even v4 gives pretty good answers to DESeq2 questions that are similar to those already posted on the support site. I've also noticed …
Answer: Important: Bioconductor Release 3.22 Delayed by shepherl 4.2k
We will continue with the release on Thursday October 30th. We have shifted one day as originally planned. Thank you
Comment: bake() and cool() resulting in an empty table by Francesc • 0
Hi Catherine, thanks so much for using dar and for reporting this bug! We have identified the issue and pushed a fix to the dar repo (PR #…
Votes
Answer: DESeq2 interactions
Answer: Important: Bioconductor Release 3.22 Delayed
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
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