Showing : Phyloseq • reset
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678
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Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 11 days ago by • 0 • written 10 months ago by • 0
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1
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2.0k
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Error with phyloseq R package with Conda install
software error phyloseq anaconda
written 7.5 years ago by • 0
2
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1
reply
985
views
Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq microbiome Software
updated 7 months ago by ★ 4.0k • written 7 months ago by ▴ 10
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0
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355
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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
8 months ago Mohamed ▴ 30
0
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6
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1.4k
views
convert default phylip to sequential phylip
phyloseq Phylogenetics
updated 12 months ago by • 0 • written 2.7 years ago by • 0
1
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1
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2.4k
views
does anyone how to create rarefaction curves from a phyloseq object?
phyloseq Phylogenetics
updated 13 months ago by ▴ 10 • written 13 months ago by • 0
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3
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1.6k
views
I cannot install "microbiome"
GenomeInfoDbData microbiome phyloseq
updated 20 months ago by 690 • written 20 months ago by • 0
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1
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657
views
error installing phyloseq
phyloseq
updated 22 months ago by 3.8k • written 22 months ago by • 0
0
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3
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869
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Controversial DESEQ2 results
phyloseq DESeq2
updated 22 months ago by 41k • written 23 months ago by • 0
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0
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492
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Association between ohylum and genus on microbiome data sets.
phyloseq
23 months ago Edmond • 0
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0
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1.3k
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How to pool phyloseq data?
phyloseq r
updated 2.1 years ago by 41k • written 2.1 years ago by • 0
0
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4
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1.8k
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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 2.1 years ago by 65k • written 2.1 years ago by • 0
0
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1
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755
views
Deseq workflow for phyloseq object and complicated data structure?
phyloseq DESeq2
updated 2.3 years ago by 41k • written 2.3 years ago by • 0
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4
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1.8k
views
Cannot install Phyloseq and dada2
GenomeInfoDbData phyloseq dada2
2.3 years ago ymtan • 0
0
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1
reply
682
views
Error in 'differential_abundance'
phyloseq devtools
updated 2.3 years ago by 41k • written 2.3 years ago by • 0
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0
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760
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Construct a phyloseq object directly from the dada2 outputs
phyloseq dada2
2.7 years ago Manijeh • 0
0
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3
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997
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DESeq2: difficulty with contrasts and main effects
DESeq2 phyloseq contrasts
updated 2.7 years ago by ★ 3.9k • written 2.7 years ago by • 0
0
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5
replies
6.4k
views
Problems with installation of 'phyloseq
phyloseq
updated 2.7 years ago by ★ 3.9k • written 2.7 years ago by • 0
0
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1
reply
684
views
Purpose of seqtabNoC
phyloseq
updated 2.8 years ago by ★ 3.9k • written 2.8 years ago by • 0
0
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3
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764
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Installing Packages repeatedly
phyloseq
updated 2.8 years ago by ★ 3.9k • written 2.8 years ago by • 0
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0
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725
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Construct Phylogenetic Tree
phyloseq
2.8 years ago klltnq • 0
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0
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618
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Code Issue
phyloseq
2.8 years ago klltnq • 0
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1
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2.1k
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Import MetaPhlAn3 to Phyloseq
Metaphlan3 Metagenomics phyloseq
updated 2.8 years ago by ★ 1.1k • written 2.8 years ago by • 0
1
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1
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3.6k
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Setting up bioconductor on a Linux server using conda
dada2 conda phyloseq
updated 3.1 years ago by 65k • written 3.1 years ago by • 0
1
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3
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1.1k
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How to assign random effect factor in DESeq2 desing?
StatisticalMethod DESeq2 phyloseq
updated 3.2 years ago by 41k • written 3.2 years ago by • 0
4
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3
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1.1k
views
Paired-test between two groups within a condition after phyloseq_to_deseq2
DESeq2 phyloseq
updated 3.2 years ago by 41k • written 3.2 years ago by ▴ 10
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0
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1.1k
views
Co-occurrence Network Analysis between Algae and Bacteria
igraph networkanalysis Phylogenetics phyloseq
3.3 years ago Chantel • 0
1
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2
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2.3k
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Bioconductor install error
phyloseq Bioconductor
3.4 years ago Tess • 0
2
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2
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1.5k
views
Bioconductor phyloseq taking forever to install?
Bioconductor phyloseq
3.5 years ago garfield320 ▴ 30
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1
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1.1k
views
Can I use pseudocounts for differential abundance of OTUs?
metagenomics deseq2 PHYLOSEQ
updated 3.7 years ago by 41k • written 3.7 years ago by • 0
0
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2
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1.9k
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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
3.8 years ago jaiber.solano.i • 0
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3
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1.0k
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Nested design- phyloseq_to_deseq
deseq2 Phyloseq Nested
updated 4.1 years ago by 41k • written 4.1 years ago by • 0
0
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2
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2.9k
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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 4.3 years ago by 25k • written 4.3 years ago by • 0
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0
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819
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Problems with creating phyloseq bar plots from a table with species data
phyloseq microbiome analysis
5.2 years ago lm795 ▴ 10
0
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2
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969
views
Phyloseq to DESeq2
deseq2 phyloseq
updated 5.3 years ago by 41k • written 5.3 years ago by • 0
0
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1
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1.5k
views
Import_biom with tree problem
phyloseq mothur 16s
5.5 years ago andrebolerbarros ▴ 20
5
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11
replies
2.8k
views
Error while installing Phyloseq using biocLite
bioclite phyloseq install error
5.5 years ago khp ▴ 30
0
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9
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2.4k
views
DESEQ2 / Phyloseq contrasts no longer work as before following update
deseq2 phyloseq
5.6 years ago eoin • 0
0
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1
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834
views
Invalid class DESeqDataSet object with Phyloseq
deseq2 phyloseq
updated 5.7 years ago by 41k • written 5.7 years ago by ▴ 10
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1
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1.7k
views
Install package phyloseq
installation phyloseq
updated 6.1 years ago by 25k • written 6.1 years ago by • 0
0
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1
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1.5k
views
tip_glom and annotations?
ggtree treeio phyloseq annotation tip_glom
updated 6.2 years ago by ★ 1.2k • written 6.2 years ago by • 0
1
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1
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1.4k
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Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
updated 6.4 years ago by 41k • written 6.4 years ago by • 0
1
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8
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5.8k
views
Cannot read Biom file
r biomformat phyloseq
updated 6.5 years ago by ★ 1.0k • written 6.5 years ago by • 0
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0
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1.2k
views
Problem with ade4 when upgrading to Rstudio 1.1 and OpenR 3.4
phyloseq installation ade4 macos
6.5 years ago sprague • 0
3
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2
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3.3k
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DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
updated 6.6 years ago by 41k • written 6.6 years ago by • 0
0
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1
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1.3k
views
phyloseq heatmap blank after multiple package updates
phyloseq heatmap
updated 6.6 years ago by ★ 13k • written 6.6 years ago by • 0
1
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3
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1.9k
views
Error bars on DESeq2 visuals
deseq2 metagenomics phyloseq ggplot2
6.7 years ago lauren.czaplicki • 0
0
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1
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1.5k
views
Phyloseq to DESeq2 with multiple variables
deseq2 phyloseq multiple time points
updated 6.8 years ago by 41k • written 6.8 years ago by • 0
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0
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1.3k
views
Phylogenetic tree from marker genes
ape phyloseq dist metagenomics
7.0 years ago David ▴ 860
1
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1
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3.5k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
7.0 years ago stats134711 • 0
50 results • Page 1 of 1
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Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Comment: get BM error by Fara • 0
Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by James W. MacDonald 65k
That's weird. I don't have any problem at all generating the `OrgDb` on my box. How big is the gene2pubmed.gz file? I get this: ``` gzip -…
Votes
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
Comment: Different Shrunk Log2FC according with reference
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
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