Showing : PHYLOSEQ • reset
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Issue when attempting to use output from DECIPHER IDtaxa (pr2 V5) with dada2/phyloseq
DECIPHER taxonomyassignment phyloseq dada2 Pr2V5
5 days ago Maggie • 0
0
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3
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1.3k
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Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 6 months ago by • 0 • written 19 months ago by • 0
2
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1
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1.7k
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Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq microbiome Software
updated 16 months ago by ★ 4.6k • written 16 months ago by ▴ 10
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0
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632
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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
17 months ago Mohamed ▴ 30
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6
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1.6k
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convert default phylip to sequential phylip
phyloseq Phylogenetics
updated 20 months ago by • 0 • written 3.4 years ago by • 0
2
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1
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4.0k
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does anyone how to create rarefaction curves from a phyloseq object?
phyloseq Phylogenetics
updated 22 months ago by ▴ 20 • written 22 months ago by • 0
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3
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2.2k
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I cannot install "microbiome"
GenomeInfoDbData microbiome phyloseq
updated 2.4 years ago by 700 • written 2.4 years ago by • 0
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1
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873
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error installing phyloseq
phyloseq
updated 2.6 years ago by 4.1k • written 2.6 years ago by • 0
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3
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1.1k
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Controversial DESEQ2 results
phyloseq DESeq2
updated 2.6 years ago by 43k • written 2.6 years ago by • 0
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0
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653
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Association between ohylum and genus on microbiome data sets.
phyloseq
2.7 years ago Edmond • 0
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1.7k
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How to pool phyloseq data?
phyloseq r
updated 2.8 years ago by 43k • written 2.8 years ago by • 0
0
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4
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2.5k
views
Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings phyloseq
updated 2.8 years ago by 67k • written 2.8 years ago by • 0
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1
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998
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Deseq workflow for phyloseq object and complicated data structure?
phyloseq DESeq2
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
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4
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2.2k
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Cannot install Phyloseq and dada2
GenomeInfoDbData phyloseq dada2
3.0 years ago ymtan • 0
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1
reply
894
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Error in 'differential_abundance'
phyloseq devtools
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
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0
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986
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Construct a phyloseq object directly from the dada2 outputs
phyloseq dada2
3.4 years ago Manijeh • 0
0
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3
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1.3k
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DESeq2: difficulty with contrasts and main effects
DESeq2 phyloseq contrasts
updated 3.4 years ago by ★ 4.0k • written 3.4 years ago by • 0
0
votes
5
replies
7.4k
views
Problems with installation of 'phyloseq
phyloseq
updated 3.4 years ago by ★ 4.0k • written 3.5 years ago by • 0
0
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1
reply
862
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Purpose of seqtabNoC
phyloseq
updated 3.6 years ago by ★ 4.0k • written 3.6 years ago by • 0
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0
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892
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Construct Phylogenetic Tree
phyloseq
3.6 years ago klltnq • 0
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0
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737
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Code Issue
phyloseq
3.6 years ago klltnq • 0
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3
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1.0k
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Installing Packages repeatedly
phyloseq
updated 3.6 years ago by ★ 4.0k • written 3.6 years ago by • 0
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1
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2.6k
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Import MetaPhlAn3 to Phyloseq
Metaphlan3 Metagenomics phyloseq
updated 3.6 years ago by ★ 1.1k • written 3.6 years ago by • 0
1
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1
reply
4.4k
views
Setting up bioconductor on a Linux server using conda
dada2 conda phyloseq
updated 3.8 years ago by 67k • written 3.8 years ago by • 0
1
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3
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1.4k
views
How to assign random effect factor in DESeq2 desing?
StatisticalMethod DESeq2 phyloseq
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
4
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3
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1.4k
views
Paired-test between two groups within a condition after phyloseq_to_deseq2
DESeq2 phyloseq
updated 3.9 years ago by 43k • written 3.9 years ago by ▴ 10
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0
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1.4k
views
Co-occurrence Network Analysis between Algae and Bacteria
igraph networkanalysis Phylogenetics phyloseq
4.0 years ago Chantel • 0
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2
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2.8k
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Bioconductor install error
phyloseq Bioconductor
4.1 years ago Tess • 0
2
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2
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2.1k
views
Bioconductor phyloseq taking forever to install?
Bioconductor phyloseq
4.2 years ago garfield320 ▴ 30
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1
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1.4k
views
Can I use pseudocounts for differential abundance of OTUs?
metagenomics deseq2 PHYLOSEQ
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
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2
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2.3k
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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
4.5 years ago jaiber.solano.i • 0
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3
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1.3k
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Nested design- phyloseq_to_deseq
deseq2 Phyloseq Nested
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
0
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2
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3.3k
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 5.1 years ago by 25k • written 5.1 years ago by • 0
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0
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1.0k
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Problems with creating phyloseq bar plots from a table with species data
phyloseq microbiome analysis
5.9 years ago lm795 ▴ 10
0
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2
replies
1.2k
views
Phyloseq to DESeq2
deseq2 phyloseq
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
0
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1
reply
1.8k
views
Import_biom with tree problem
phyloseq mothur 16s
6.2 years ago andrebolerbarros ▴ 20
5
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11
replies
3.1k
views
Error while installing Phyloseq using biocLite
bioclite phyloseq install error
6.3 years ago khp ▴ 30
0
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9
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2.8k
views
DESEQ2 / Phyloseq contrasts no longer work as before following update
deseq2 phyloseq
6.3 years ago eoin • 0
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1
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1.0k
views
Invalid class DESeqDataSet object with Phyloseq
deseq2 phyloseq
updated 6.4 years ago by 43k • written 6.4 years ago by ▴ 10
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1
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2.0k
views
Install package phyloseq
installation phyloseq
updated 6.8 years ago by 25k • written 6.8 years ago by • 0
0
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1
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1.9k
views
tip_glom and annotations?
ggtree treeio phyloseq annotation tip_glom
updated 6.9 years ago by ★ 1.2k • written 6.9 years ago by • 0
1
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1
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1.6k
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
1
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8
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6.6k
views
Cannot read Biom file
r biomformat phyloseq
updated 7.2 years ago by ★ 1.0k • written 7.2 years ago by • 0
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0
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1.5k
views
Problem with ade4 when upgrading to Rstudio 1.1 and OpenR 3.4
phyloseq installation ade4 macos
7.2 years ago sprague • 0
3
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2
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3.9k
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DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
0
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1
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1.6k
views
phyloseq heatmap blank after multiple package updates
phyloseq heatmap
updated 7.4 years ago by ★ 13k • written 7.4 years ago by • 0
1
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3
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2.2k
views
Error bars on DESeq2 visuals
deseq2 metagenomics phyloseq ggplot2
7.4 years ago lauren.czaplicki • 0
0
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1
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1.8k
views
Phyloseq to DESeq2 with multiple variables
deseq2 phyloseq multiple time points
updated 7.5 years ago by 43k • written 7.5 years ago by • 0
0
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0
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1.5k
views
Phylogenetic tree from marker genes
ape phyloseq dist metagenomics
7.7 years ago David ▴ 860
1
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1
reply
3.9k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
7.8 years ago stats134711 • 0
50 results • Page 1 of 1
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Answer: promoters_txdb <- promoters(txdb, upstream = 2000) is not 2000 by James W. MacDonald 67k
If you use `promoters` and do not provide an argument for something that has a default, you will get the default argument. Your last call t…
Comment: org.Hs.eg.db issue by k.panov • 0
installed R on another PC, works perfectly. ergo, problem outside of R probably..... :-(
Comment: MBDseq analysis using qsea package by Lukas ▴ 20
Hi, I checked in with Matthias and here is his response: You need to indicate "samples": "The indices of the samples for which individu…
Comment: DESeq2 analysis with transcript counts by sindhuri • 0
Thank you for the response. Currently I am using the R studio for analysis and Im running DESeq2 for analysis of the **transcript counts.ts…
Comment: iam not able to do retrive data using GEOquery R package by James W. MacDonald 67k
Another alternative is to use the `GEOmetadb` package ([vignette here)][1], which will allow you to make queries to identify GEO datasets t…
Votes
Answer: Is there any chance to solve "the model matrix is not full rank" in DESeq2?
Answer: Issue carrying out DiffBind Analysis at a predefined peak set
Answer: Differential variability modelling with vst() expression
Answer: Differential variability modelling with vst() expression
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
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