Showing : phyloseq • reset
0
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3
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1.2k
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Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 5 months ago by • 0 • written 18 months ago by • 0
2
votes
1
reply
1.6k
views
Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq microbiome Software
updated 15 months ago by ★ 4.6k • written 15 months ago by ▴ 10
0
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0
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610
views
Try to understand better how to set out an effective sample size within the MetagenomSeq package in microbiome ?
Metagenomics metagenomeSeq microbiome phyloseq microbiomeDataSets
16 months ago Mohamed ▴ 30
0
votes
6
replies
1.6k
views
convert default phylip to sequential phylip
phyloseq Phylogenetics
updated 20 months ago by • 0 • written 3.3 years ago by • 0
2
votes
1
reply
3.9k
views
does anyone how to create rarefaction curves from a phyloseq object?
phyloseq Phylogenetics
updated 21 months ago by ▴ 20 • written 21 months ago by • 0
0
votes
3
replies
2.2k
views
I cannot install "microbiome"
GenomeInfoDbData microbiome phyloseq
updated 2.4 years ago by 700 • written 2.4 years ago by • 0
0
votes
1
reply
862
views
error installing phyloseq
phyloseq
updated 2.5 years ago by 4.1k • written 2.5 years ago by • 0
0
votes
3
replies
1.1k
views
Controversial DESEQ2 results
phyloseq DESeq2
updated 2.5 years ago by 43k • written 2.6 years ago by • 0
0
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0
replies
643
views
Association between ohylum and genus on microbiome data sets.
phyloseq
2.6 years ago Edmond • 0
0
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0
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1.7k
views
How to pool phyloseq data?
phyloseq r
updated 2.7 years ago by 43k • written 2.8 years ago by • 0
0
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4
replies
2.4k
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
0
votes
1
reply
980
views
Deseq workflow for phyloseq object and complicated data structure?
phyloseq DESeq2
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
0
votes
4
replies
2.2k
views
Cannot install Phyloseq and dada2
GenomeInfoDbData phyloseq dada2
2.9 years ago ymtan • 0
0
votes
1
reply
883
views
Error in 'differential_abundance'
phyloseq devtools
updated 2.9 years ago by 43k • written 3.0 years ago by • 0
0
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0
replies
974
views
Construct a phyloseq object directly from the dada2 outputs
phyloseq dada2
3.3 years ago Manijeh • 0
0
votes
3
replies
1.3k
views
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
7.3k
views
Problems with installation of 'phyloseq
phyloseq
updated 3.4 years ago by ★ 4.0k • written 3.4 years ago by • 0
0
votes
1
reply
854
views
Purpose of seqtabNoC
phyloseq
updated 3.5 years ago by ★ 4.0k • written 3.5 years ago by • 0
0
votes
0
replies
880
views
Construct Phylogenetic Tree
phyloseq
3.5 years ago klltnq • 0
0
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0
replies
730
views
Code Issue
phyloseq
3.5 years ago klltnq • 0
0
votes
3
replies
993
views
Installing Packages repeatedly
phyloseq
updated 3.5 years ago by ★ 4.0k • written 3.5 years ago by • 0
0
votes
1
reply
2.6k
views
Import MetaPhlAn3 to Phyloseq
Metaphlan3 Metagenomics phyloseq
updated 3.5 years ago by ★ 1.1k • written 3.5 years ago by • 0
1
vote
1
reply
4.4k
views
Setting up bioconductor on a Linux server using conda
dada2 conda phyloseq
updated 3.7 years ago by 67k • written 3.7 years ago by • 0
1
vote
3
replies
1.4k
views
How to assign random effect factor in DESeq2 desing?
StatisticalMethod DESeq2 phyloseq
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
4
votes
3
replies
1.4k
views
Paired-test between two groups within a condition after phyloseq_to_deseq2
DESeq2 phyloseq
updated 3.8 years ago by 43k • written 3.8 years ago by ▴ 10
0
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0
replies
1.3k
views
Co-occurrence Network Analysis between Algae and Bacteria
igraph networkanalysis Phylogenetics phyloseq
3.9 years ago Chantel • 0
1
vote
2
replies
2.8k
views
Bioconductor install error
phyloseq Bioconductor
4.1 years ago Tess • 0
2
votes
2
replies
2.1k
views
Bioconductor phyloseq taking forever to install?
Bioconductor phyloseq
4.1 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 4.4 years ago by 43k • written 4.4 years ago by • 0
0
votes
2
replies
2.3k
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
4.5 years ago jaiber.solano.i • 0
0
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3
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1.3k
views
Nested design- phyloseq_to_deseq
deseq2 Phyloseq Nested
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
0
votes
2
replies
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 5.0 years ago by 25k • written 5.0 years ago by • 0
0
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0
replies
997
views
Problems with creating phyloseq bar plots from a table with species data
phyloseq microbiome analysis
5.9 years ago lm795 ▴ 10
0
votes
2
replies
1.2k
views
Phyloseq to DESeq2
deseq2 phyloseq
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
0
votes
1
reply
1.8k
views
Import_biom with tree problem
phyloseq mothur 16s
6.2 years ago andrebolerbarros ▴ 20
5
votes
11
replies
3.0k
views
Error while installing Phyloseq using biocLite
bioclite phyloseq install error
6.2 years ago khp ▴ 30
0
votes
9
replies
2.8k
views
DESEQ2 / Phyloseq contrasts no longer work as before following update
deseq2 phyloseq
6.3 years ago eoin • 0
0
votes
1
reply
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
0
votes
1
reply
2.0k
views
Install package phyloseq
installation phyloseq
updated 6.8 years ago by 25k • written 6.8 years ago by • 0
0
votes
1
reply
1.8k
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
vote
1
reply
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
vote
8
replies
6.6k
views
Cannot read Biom file
r biomformat phyloseq
updated 7.1 years ago by ★ 1.0k • written 7.1 years ago by • 0
0
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0
replies
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
votes
2
replies
3.8k
views
DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
0
votes
1
reply
1.5k
views
phyloseq heatmap blank after multiple package updates
phyloseq heatmap
updated 7.3 years ago by ★ 13k • written 7.3 years ago by • 0
1
vote
3
replies
2.2k
views
Error bars on DESeq2 visuals
deseq2 metagenomics phyloseq ggplot2
7.3 years ago lauren.czaplicki • 0
0
votes
1
reply
1.8k
views
Phyloseq to DESeq2 with multiple variables
deseq2 phyloseq multiple time points
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
0
votes
0
replies
1.5k
views
Phylogenetic tree from marker genes
ape phyloseq dist metagenomics
7.7 years ago David ▴ 860
1
vote
1
reply
3.9k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
7.7 years ago stats134711 • 0
0
votes
1
reply
2.3k
views
ggtree facet_plot question using geom_boxplot to plot abundance data corresponding to tree tips
ggtree ggplot2 phyloseq geom_boxplot facet_plot
updated 7.8 years ago by ★ 1.2k • written 7.8 years ago by • 0
50 results • Page 1 of 1
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Comment: ISO a solution to rank-order introns by transcript by mat149 ▴ 80
Hey, In revisiting this question, the following code works for the '+' strand. I am having issues with demarcating intron rank by transcri…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by Gordon Smyth 52k
Since the intra-block correlation is negative, it would be best to remove `block` from the model. My experience with genetically identical…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by anna.cot.anna.cot ▴ 30
Thank you! This is actually quite close to my real dataset. I simplified the names to make it easier as an example, but I have now correcte…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Tim Peters ▴ 200
Hi Xiaofei, Is it possible to generate a matrix of beta values or M-values with rownames as probe IDs from this data? If so, cpg.annotate(…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by Gordon Smyth 52k
That looks basically correct, although the terms that you are inputing to `makeContrasts` do not match the condition names in the targets f…
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Answer: nightmare to make custom txdb for genomes from ToxoDB
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