Showing : PHYLOSEQ • reset
2
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405
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Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq microbiome Software
updated 10 weeks ago by ★ 3.6k • written 10 weeks ago by ▴ 10
0
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0
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207
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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
3 months ago Mohamed ▴ 20
0
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1
reply
349
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Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
written 5 months ago by • 0
0
votes
6
replies
1.2k
views
convert default phylip to sequential phylip
phyloseq Phylogenetics
updated 7 months ago by • 0 • written 2.3 years ago by • 0
1
vote
1
reply
1.5k
views
does anyone how to create rarefaction curves from a phyloseq object?
phyloseq Phylogenetics
updated 8 months ago by ▴ 10 • written 8 months ago by • 0
0
votes
3
replies
1.2k
views
I cannot install "microbiome"
GenomeInfoDbData microbiome phyloseq
updated 15 months ago by 680 • written 15 months ago by • 0
0
votes
1
reply
528
views
error installing phyloseq
phyloseq
updated 17 months ago by 3.6k • written 17 months ago by • 0
0
votes
3
replies
716
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Controversial DESEQ2 results
phyloseq DESeq2
updated 18 months ago by 41k • written 18 months ago by • 0
0
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0
replies
392
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Association between ohylum and genus on microbiome data sets.
phyloseq
19 months ago Edmond • 0
0
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0
replies
1.1k
views
How to pool phyloseq data?
phyloseq r
updated 20 months ago by 41k • written 20 months ago by • 0
0
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4
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1.4k
views
Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings phyloseq
updated 20 months ago by 64k • written 20 months ago by • 0
0
votes
1
reply
641
views
Deseq workflow for phyloseq object and complicated data structure?
phyloseq DESeq2
updated 22 months ago by 41k • written 22 months ago by • 0
0
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4
replies
1.5k
views
Cannot install Phyloseq and dada2
GenomeInfoDbData phyloseq dada2
22 months ago ymtan • 0
0
votes
1
reply
556
views
Error in 'differential_abundance'
phyloseq devtools
updated 23 months ago by 41k • written 23 months ago by • 0
0
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0
replies
646
views
Construct a phyloseq object directly from the dada2 outputs
phyloseq dada2
2.3 years ago Manijeh • 0
0
votes
3
replies
823
views
DESeq2: difficulty with contrasts and main effects
DESeq2 phyloseq contrasts
updated 2.3 years ago by 3.9k • written 2.3 years ago by • 0
0
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5
replies
5.4k
views
Problems with installation of 'phyloseq
phyloseq
updated 2.3 years ago by 3.9k • written 2.3 years ago by • 0
0
votes
1
reply
580
views
Purpose of seqtabNoC
phyloseq
updated 2.4 years ago by 3.9k • written 2.4 years ago by • 0
0
votes
0
replies
608
views
Construct Phylogenetic Tree
phyloseq
2.4 years ago klltnq • 0
0
votes
0
replies
524
views
Code Issue
phyloseq
2.4 years ago klltnq • 0
0
votes
3
replies
657
views
Installing Packages repeatedly
phyloseq
updated 2.4 years ago by 3.9k • written 2.4 years ago by • 0
0
votes
1
reply
1.8k
views
Import MetaPhlAn3 to Phyloseq
Metaphlan3 Metagenomics phyloseq
updated 2.4 years ago by 1.1k • written 2.4 years ago by • 0
1
vote
1
reply
3.1k
views
Setting up bioconductor on a Linux server using conda
dada2 conda phyloseq
updated 2.7 years ago by 64k • written 2.7 years ago by • 0
1
vote
3
replies
912
views
How to assign random effect factor in DESeq2 desing?
StatisticalMethod DESeq2 phyloseq
updated 2.8 years ago by 41k • written 2.8 years ago by • 0
4
votes
3
replies
956
views
Paired-test between two groups within a condition after phyloseq_to_deseq2
DESeq2 phyloseq
updated 2.8 years ago by 41k • written 2.8 years ago by ▴ 10
0
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0
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917
views
Co-occurrence Network Analysis between Algae and Bacteria
igraph networkanalysis Phylogenetics phyloseq
2.9 years ago Chantel • 0
1
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2
replies
2.0k
views
Bioconductor install error
phyloseq Bioconductor
3.0 years ago Tess • 0
2
votes
2
replies
1.3k
views
Bioconductor phyloseq taking forever to install?
Bioconductor phyloseq
3.1 years ago garfield320 ▴ 30
0
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1
reply
983
views
Can I use pseudocounts for differential abundance of OTUs?
metagenomics deseq2 PHYLOSEQ
updated 3.3 years ago by 41k • written 3.3 years ago by • 0
0
votes
2
replies
1.6k
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
3.4 years ago jaiber.solano.i • 0
0
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3
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865
views
Nested design- phyloseq_to_deseq
deseq2 Phyloseq Nested
updated 3.7 years ago by 41k • written 3.7 years ago by • 0
0
votes
2
replies
2.6k
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 3.9 years ago by 25k • written 3.9 years ago by • 0
0
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0
replies
706
views
Problems with creating phyloseq bar plots from a table with species data
phyloseq microbiome analysis
4.8 years ago lm795 ▴ 10
0
votes
2
replies
866
views
Phyloseq to DESeq2
deseq2 phyloseq
updated 4.9 years ago by 41k • written 4.9 years ago by • 0
0
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1
reply
1.3k
views
Import_biom with tree problem
phyloseq mothur 16s
5.1 years ago andrebolerbarros ▴ 20
5
votes
11
replies
2.5k
views
Error while installing Phyloseq using biocLite
bioclite phyloseq install error
5.1 years ago khp ▴ 30
0
votes
9
replies
2.2k
views
DESEQ2 / Phyloseq contrasts no longer work as before following update
deseq2 phyloseq
5.2 years ago eoin • 0
0
votes
1
reply
705
views
Invalid class DESeqDataSet object with Phyloseq
deseq2 phyloseq
updated 5.3 years ago by 41k • written 5.3 years ago by ▴ 10
0
votes
1
reply
1.5k
views
Install package phyloseq
installation phyloseq
updated 5.7 years ago by 25k • written 5.7 years ago by • 0
0
votes
1
reply
1.3k
views
tip_glom and annotations?
ggtree treeio phyloseq annotation tip_glom
updated 5.8 years ago by ★ 1.2k • written 5.8 years ago by • 0
1
vote
1
reply
1.2k
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
updated 6.0 years ago by 41k • written 6.0 years ago by • 0
1
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8
replies
5.2k
views
Cannot read Biom file
r biomformat phyloseq
updated 6.1 years ago by ▴ 990 • written 6.1 years ago by • 0
0
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0
replies
1.1k
views
Problem with ade4 when upgrading to Rstudio 1.1 and OpenR 3.4
phyloseq installation ade4 macos
6.1 years ago sprague • 0
3
votes
2
replies
2.9k
views
DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
updated 6.2 years ago by 41k • written 6.2 years ago by • 0
0
votes
1
reply
1.2k
views
phyloseq heatmap blank after multiple package updates
phyloseq heatmap
updated 6.2 years ago by 13k • written 6.2 years ago by • 0
1
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3
replies
1.7k
views
Error bars on DESeq2 visuals
deseq2 metagenomics phyloseq ggplot2
6.3 years ago lauren.czaplicki • 0
0
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1
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1.4k
views
Phyloseq to DESeq2 with multiple variables
deseq2 phyloseq multiple time points
updated 6.4 years ago by 41k • written 6.4 years ago by • 0
0
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0
replies
1.2k
views
Phylogenetic tree from marker genes
ape phyloseq dist metagenomics
6.6 years ago David ▴ 860
1
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1
reply
3.2k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
6.6 years ago stats134711 • 0
0
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1
reply
1.9k
views
ggtree facet_plot question using geom_boxplot to plot abundance data corresponding to tree tips
ggtree ggplot2 phyloseq geom_boxplot facet_plot
updated 6.7 years ago by ★ 1.2k • written 6.7 years ago by • 0
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Comment: NCBI protein to NCBI cDNA (Ensembl conversions would be great as well) in R by James W. MacDonald 64k
It does look like CBP2 is an HGNC symbol, not a protein ID though. ``` > z <- select(ws, "CPB2", c("gene_names","xref_geneid","xref_ensemb…
Comment: How can I avoid artifacts in gene set/pathway scoring by UCell and similar algor by arina • 0
Hi Omer, Unfortunately I don't have an answer to your issue, but I am facing a very similar problem after integrating datasets that were …
Answer: NCBI protein to NCBI cDNA (Ensembl conversions would be great as well) in R by James W. MacDonald 64k
I don't know what you mean by 'cDNA value'. That could mean any number of things, I suppose, particularly if you don't know what cDNA is (p…
Comment: How can we use the organism database created by makeorgPackageFromNCBI to KEGG a by Guido Hooiveld ★ 3.8k
What did you try yourselves? Again, please show your code....!! For KEGG-based analysis you can make use of the convenience functions `enr…
Comment: Deleted:No significant MVPs with a BH adjusted P-value below 0.05 by Basti ▴ 740
The image is blurred, but you need to follow ATpoint advice and restart the entire analysis using a clean environment.
Votes
A: DSS understanding delta option and posterior probability
Comment: Ensembl down???
Answer: How should I run ssGSEA Hallmark Enrichment Analysis?
Answer: tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
Comment: Problem loading HDF5Array in R 4.3.2
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