Showing : PHYLOSEQ • reset
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How can I correctly use phyloseq with Docker?
phylo phyloseq Docker
written 5 months ago by • 0
0
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1
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373
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DESeq2 from phyloseq error
DESeq2 phyloseq
4 months ago asafpr • 0
0
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2
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844
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Issue when attempting to use output from DECIPHER IDtaxa (pr2 V5) with dada2/phyloseq
DECIPHER taxonomyassignment phyloseq dada2 Pr2V5
updated 6 months ago by • 0 • written 8 months ago by • 0
0
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3
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1.7k
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Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 14 months ago by • 0 • written 2.3 years ago by • 0
2
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1
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2.3k
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Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq microbiome Software
updated 2.0 years ago by ★ 4.9k • written 2.0 years ago by ▴ 10
0
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0
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798
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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
2.1 years ago Mohamed ▴ 30
0
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6
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1.8k
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convert default phylip to sequential phylip
phyloseq Phylogenetics
updated 2.4 years ago by • 0 • written 4.1 years ago by • 0
2
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1
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5.4k
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does anyone how to create rarefaction curves from a phyloseq object?
phyloseq Phylogenetics
updated 2.5 years ago by ▴ 20 • written 2.5 years ago by • 0
0
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3
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2.6k
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I cannot install "microbiome"
GenomeInfoDbData microbiome phyloseq
updated 3.1 years ago by 700 • written 3.2 years ago by • 0
0
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1
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1.1k
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error installing phyloseq
phyloseq
updated 3.3 years ago by 4.2k • written 3.3 years ago by • 0
0
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3
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1.4k
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Controversial DESEQ2 results
phyloseq DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
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0
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824
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Association between ohylum and genus on microbiome data sets.
phyloseq
3.4 years ago Edmond • 0
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0
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2.0k
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How to pool phyloseq data?
phyloseq r
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
0
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4
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3.0k
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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 3.6 years ago by 68k • written 3.6 years ago by • 0
0
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1
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1.2k
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Deseq workflow for phyloseq object and complicated data structure?
phyloseq DESeq2
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
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4
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2.6k
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Cannot install Phyloseq and dada2
GenomeInfoDbData phyloseq dada2
3.7 years ago ymtan • 0
0
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1
reply
1.1k
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Error in 'differential_abundance'
phyloseq devtools
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
0
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0
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1.2k
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Construct a phyloseq object directly from the dada2 outputs
phyloseq dada2
4.1 years ago Manijeh • 0
0
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3
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1.6k
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DESeq2: difficulty with contrasts and main effects
DESeq2 phyloseq contrasts
updated 4.2 years ago by ★ 4.0k • written 4.2 years ago by • 0
0
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5
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8.2k
views
Problems with installation of 'phyloseq
phyloseq
updated 4.2 years ago by ★ 4.0k • written 4.2 years ago by • 0
0
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1
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1.0k
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Purpose of seqtabNoC
phyloseq
updated 4.3 years ago by ★ 4.0k • written 4.3 years ago by • 0
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0
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1.1k
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Construct Phylogenetic Tree
phyloseq
4.3 years ago klltnq • 0
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0
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849
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Code Issue
phyloseq
4.3 years ago klltnq • 0
0
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3
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1.2k
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Installing Packages repeatedly
phyloseq
updated 4.3 years ago by ★ 4.0k • written 4.3 years ago by • 0
0
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1
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3.0k
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Import MetaPhlAn3 to Phyloseq
Metaphlan3 Metagenomics phyloseq
updated 4.3 years ago by ★ 1.1k • written 4.3 years ago by • 0
1
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1
reply
5.3k
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Setting up bioconductor on a Linux server using conda
dada2 conda phyloseq
updated 4.5 years ago by 68k • written 4.5 years ago by • 0
1
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3
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1.6k
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How to assign random effect factor in DESeq2 desing?
StatisticalMethod DESeq2 phyloseq
updated 4.6 years ago by 43k • written 4.6 years ago by • 0
4
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3
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1.6k
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Paired-test between two groups within a condition after phyloseq_to_deseq2
DESeq2 phyloseq
updated 4.6 years ago by 43k • written 4.6 years ago by ▴ 10
0
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1
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1.8k
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Co-occurrence Network Analysis between Algae and Bacteria
igraph networkanalysis Phylogenetics phyloseq
updated 6 months ago by • 0 • written 4.7 years ago by • 0
1
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2
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3.2k
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Bioconductor install error
phyloseq Bioconductor
4.9 years ago Tess • 0
2
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2
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2.7k
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Bioconductor phyloseq taking forever to install?
Bioconductor phyloseq
4.9 years ago garfield320 ▴ 30
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1
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1.7k
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Can I use pseudocounts for differential abundance of OTUs?
metagenomics deseq2 PHYLOSEQ
updated 5.2 years ago by 43k • written 5.2 years ago by • 0
0
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2
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2.7k
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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
5.3 years ago • updated 5.2 years ago jaiber.solano.i • 0
0
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3
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1.5k
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Nested design- phyloseq_to_deseq
deseq2 Phyloseq Nested
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
0
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2
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3.6k
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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 5.8 years ago by 25k • written 5.8 years ago by • 0
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0
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1.2k
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Problems with creating phyloseq bar plots from a table with species data
phyloseq microbiome analysis
6.6 years ago lm795 ▴ 10
0
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2
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1.4k
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Phyloseq to DESeq2
deseq2 phyloseq
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
0
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1
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2.0k
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Import_biom with tree problem
phyloseq mothur 16s
7.0 years ago andrebolerbarros ▴ 20
5
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11
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3.5k
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Error while installing Phyloseq using biocLite
bioclite phyloseq install error
7.0 years ago khp ▴ 30
0
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9
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3.1k
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DESEQ2 / Phyloseq contrasts no longer work as before following update
deseq2 phyloseq
7.0 years ago eoin • 0
0
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1
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1.3k
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Invalid class DESeqDataSet object with Phyloseq
deseq2 phyloseq
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 10
0
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1
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2.3k
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Install package phyloseq
installation phyloseq
updated 7.6 years ago by 25k • written 7.6 years ago by • 0
0
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1
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2.2k
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tip_glom and annotations?
ggtree treeio phyloseq annotation tip_glom
updated 7.7 years ago by ★ 1.2k • written 7.7 years ago by • 0
1
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1
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1.8k
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Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
1
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8
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7.3k
views
Cannot read Biom file
r biomformat phyloseq
updated 7.9 years ago by ★ 1.1k • written 7.9 years ago by • 0
0
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0
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1.8k
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Problem with ade4 when upgrading to Rstudio 1.1 and OpenR 3.4
phyloseq installation ade4 macos
8.0 years ago sprague • 0
3
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2
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4.2k
views
DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
updated 8.1 years ago by 43k • written 8.1 years ago by • 0
0
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1
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1.8k
views
phyloseq heatmap blank after multiple package updates
phyloseq heatmap
updated 8.1 years ago by ★ 13k • written 8.1 years ago by • 0
1
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3
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2.5k
views
Error bars on DESeq2 visuals
deseq2 metagenomics phyloseq ggplot2
8.1 years ago lauren.czaplicki • 0
0
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1
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2.0k
views
Phyloseq to DESeq2 with multiple variables
deseq2 phyloseq multiple time points
updated 8.2 years ago by 43k • written 8.2 years ago by • 0
76 results • Page 1 of 2
Recent ...
Replies
Answer: Gatins Set error by James W. MacDonald 68k
`GatingSet` isn't a function in `flowCore`. It is however in `flowWorkspace`, which you would need to load first.
Answer: How to model DE for RNA-seq in concordant monozygotic twins? by Gordon Smyth 53k
Your question is more about science than it is about software syntax, and I can't give advice about how to conduct a scientific analysis, n…
Comment: incomplete imputation of missing values with LEA impute() function by Gordon Smyth 53k
Nadia, please tag your question with the name of the package ("LEA") that you are asking about. "impute" is the name of a different Biocond…
Comment: Sharing a collection of datasets in ExperimentHub by Aaron Lun ★ 29k
FYI the **scRNAseq** packages uses a non-ExperimentHub storage platform, see [here](https://github.com/ArtifactDB/gypsum-worker) for more d…
Comment: Error Loading Experiment from SimBenchData Package by ATpoint ★ 4.9k
Is the Seurat package installed? The error somewhat suggests that it could be related, and at https://www.bioconductor.org/packages/release…
Votes
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
Answer: ordinary t from limma [was: How would I normally compare swirl?]
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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