Showing : Phyloseq • reset
0
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3
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1.1k
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Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 8 weeks ago by • 0 • written 15 months ago by • 0
2
votes
1
reply
1.4k
views
Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq microbiome Software
updated 11 months ago by ★ 4.4k • written 11 months ago by ▴ 10
0
votes
0
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527
views
Try to understand better how to set out an effective sample size within the MetagenomSeq package in microbiome ?
Metagenomics metagenomeSeq microbiome phyloseq microbiomeDataSets
12 months ago Mohamed ▴ 30
0
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6
replies
1.5k
views
convert default phylip to sequential phylip
phyloseq Phylogenetics
updated 16 months ago by • 0 • written 3.0 years ago by • 0
1
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1
reply
3.3k
views
does anyone how to create rarefaction curves from a phyloseq object?
phyloseq Phylogenetics
updated 17 months ago by ▴ 10 • written 17 months ago by • 0
0
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3
replies
2.0k
views
I cannot install "microbiome"
GenomeInfoDbData microbiome phyloseq
updated 2.1 years ago by 700 • written 2.1 years ago by • 0
0
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1
reply
785
views
error installing phyloseq
phyloseq
updated 2.2 years ago by 4.0k • written 2.2 years ago by • 0
0
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3
replies
1.1k
views
Controversial DESEQ2 results
phyloseq DESeq2
updated 2.3 years ago by 42k • written 2.3 years ago by • 0
0
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0
replies
587
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Association between ohylum and genus on microbiome data sets.
phyloseq
2.4 years ago Edmond • 0
0
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0
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1.6k
views
How to pool phyloseq data?
phyloseq r
updated 2.5 years ago by 42k • written 2.5 years ago by • 0
0
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4
replies
2.2k
views
Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings phyloseq
updated 2.5 years ago by 67k • written 2.5 years ago by • 0
0
votes
1
reply
904
views
Deseq workflow for phyloseq object and complicated data structure?
phyloseq DESeq2
updated 2.6 years ago by 42k • written 2.6 years ago by • 0
0
votes
4
replies
2.0k
views
Cannot install Phyloseq and dada2
GenomeInfoDbData phyloseq dada2
2.6 years ago ymtan • 0
0
votes
1
reply
811
views
Error in 'differential_abundance'
phyloseq devtools
updated 2.7 years ago by 42k • written 2.7 years ago by • 0
0
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0
replies
903
views
Construct a phyloseq object directly from the dada2 outputs
phyloseq dada2
3.1 years ago Manijeh • 0
0
votes
3
replies
1.2k
views
DESeq2: difficulty with contrasts and main effects
DESeq2 phyloseq contrasts
updated 3.1 years ago by ★ 4.0k • written 3.1 years ago by • 0
0
votes
5
replies
7.0k
views
Problems with installation of 'phyloseq
phyloseq
updated 3.1 years ago by ★ 4.0k • written 3.1 years ago by • 0
0
votes
1
reply
793
views
Purpose of seqtabNoC
phyloseq
updated 3.2 years ago by ★ 4.0k • written 3.2 years ago by • 0
0
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0
replies
828
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Construct Phylogenetic Tree
phyloseq
3.2 years ago klltnq • 0
0
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0
replies
684
views
Code Issue
phyloseq
3.2 years ago klltnq • 0
0
votes
3
replies
929
views
Installing Packages repeatedly
phyloseq
updated 3.2 years ago by ★ 4.0k • written 3.2 years ago by • 0
0
votes
1
reply
2.5k
views
Import MetaPhlAn3 to Phyloseq
Metaphlan3 Metagenomics phyloseq
updated 3.2 years ago by ★ 1.1k • written 3.2 years ago by • 0
1
vote
1
reply
4.1k
views
Setting up bioconductor on a Linux server using conda
dada2 conda phyloseq
updated 3.5 years ago by 67k • written 3.5 years ago by • 0
1
vote
3
replies
1.3k
views
How to assign random effect factor in DESeq2 desing?
StatisticalMethod DESeq2 phyloseq
updated 3.6 years ago by 42k • written 3.6 years ago by • 0
4
votes
3
replies
1.3k
views
Paired-test between two groups within a condition after phyloseq_to_deseq2
DESeq2 phyloseq
updated 3.6 years ago by 42k • written 3.6 years ago by ▴ 10
0
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0
replies
1.2k
views
Co-occurrence Network Analysis between Algae and Bacteria
igraph networkanalysis Phylogenetics phyloseq
3.7 years ago Chantel • 0
1
vote
2
replies
2.6k
views
Bioconductor install error
phyloseq Bioconductor
3.8 years ago Tess • 0
2
votes
2
replies
1.9k
views
Bioconductor phyloseq taking forever to install?
Bioconductor phyloseq
3.9 years ago garfield320 ▴ 30
0
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1
reply
1.3k
views
Can I use pseudocounts for differential abundance of OTUs?
metagenomics deseq2 PHYLOSEQ
updated 4.1 years ago by 42k • written 4.1 years ago by • 0
0
votes
2
replies
2.1k
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
4.2 years ago jaiber.solano.i • 0
0
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3
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1.2k
views
Nested design- phyloseq_to_deseq
deseq2 Phyloseq Nested
updated 4.4 years ago by 42k • written 4.4 years ago by • 0
0
votes
2
replies
3.1k
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 4.7 years ago by 25k • written 4.7 years ago by • 0
0
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0
replies
925
views
Problems with creating phyloseq bar plots from a table with species data
phyloseq microbiome analysis
5.6 years ago lm795 ▴ 10
0
votes
2
replies
1.1k
views
Phyloseq to DESeq2
deseq2 phyloseq
updated 5.6 years ago by 42k • written 5.6 years ago by • 0
0
votes
1
reply
1.7k
views
Import_biom with tree problem
phyloseq mothur 16s
5.9 years ago andrebolerbarros ▴ 20
5
votes
11
replies
2.9k
views
Error while installing Phyloseq using biocLite
bioclite phyloseq install error
5.9 years ago khp ▴ 30
0
votes
9
replies
2.6k
views
DESEQ2 / Phyloseq contrasts no longer work as before following update
deseq2 phyloseq
6.0 years ago eoin • 0
0
votes
1
reply
953
views
Invalid class DESeqDataSet object with Phyloseq
deseq2 phyloseq
updated 6.1 years ago by 42k • written 6.1 years ago by ▴ 10
0
votes
1
reply
1.8k
views
Install package phyloseq
installation phyloseq
updated 6.5 years ago by 25k • written 6.5 years ago by • 0
0
votes
1
reply
1.7k
views
tip_glom and annotations?
ggtree treeio phyloseq annotation tip_glom
updated 6.6 years ago by ★ 1.2k • written 6.6 years ago by • 0
1
vote
1
reply
1.5k
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
updated 6.8 years ago by 42k • written 6.8 years ago by • 0
1
vote
8
replies
6.3k
views
Cannot read Biom file
r biomformat phyloseq
updated 6.9 years ago by ★ 1.0k • written 6.9 years ago by • 0
0
votes
0
replies
1.4k
views
Problem with ade4 when upgrading to Rstudio 1.1 and OpenR 3.4
phyloseq installation ade4 macos
6.9 years ago sprague • 0
3
votes
2
replies
3.6k
views
DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
updated 7.0 years ago by 42k • written 7.0 years ago by • 0
0
votes
1
reply
1.5k
views
phyloseq heatmap blank after multiple package updates
phyloseq heatmap
updated 7.0 years ago by ★ 13k • written 7.0 years ago by • 0
1
vote
3
replies
2.1k
views
Error bars on DESeq2 visuals
deseq2 metagenomics phyloseq ggplot2
7.1 years ago lauren.czaplicki • 0
0
votes
1
reply
1.7k
views
Phyloseq to DESeq2 with multiple variables
deseq2 phyloseq multiple time points
updated 7.2 years ago by 42k • written 7.2 years ago by • 0
0
votes
0
replies
1.4k
views
Phylogenetic tree from marker genes
ape phyloseq dist metagenomics
7.4 years ago David ▴ 860
1
vote
1
reply
3.7k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
7.4 years ago stats134711 • 0
0
votes
1
reply
2.2k
views
ggtree facet_plot question using geom_boxplot to plot abundance data corresponding to tree tips
ggtree ggplot2 phyloseq geom_boxplot facet_plot
updated 7.5 years ago by ★ 1.2k • written 7.5 years ago by • 0
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Comment: AffylmGUI does not start wit R 4.4.1 by Gordon Smyth 51k
affylmGUI passes all checks for all platforms, including Mac OS and arm64, for Bioconductor 3.20, so I assume it must work on a Mac: htt…
Comment: ı cant install clusterprofiler on my Ubuntu 20.04.6 LTS by semra • 0
install(Biostrings, force = TRUE) Error in install(Biostrings, force = TRUE) : install fonksiyonu bulunamadı > library(Biostrings) Erro…
Comment: AffylmGUI does not start wit R 4.4.1 by richardallenfriedmanbrooklyn ▴ 20
Dear List, AffylmGUI works fine with R 4.4.1 on Windows. However most of my students have macs. I have installed BWidget and Tktable in the…
Answer: PCA analysis RNA-Seq QC looks strange? by swbarnes2 ★ 1.4k
In my experience, when the first PC is 91% of the difference, its because you are looking at two different tissues. Check to see what gene…
Comment: ı cant install clusterprofiler on my Ubuntu 20.04.6 LTS by James W. MacDonald 67k
What is the output from ``` install("Biostrings, force = TRUE) library(Biostrings) ```
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Time course experiment using limma
DEXseq: How to do differential exon usage of genes with overlapping exons
A: Moderated F-test followed by moderated t-test in limma
Answer: [DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Applic
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