Showing : PHYLOSEQ • reset
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Issue when attempting to use output from DECIPHER IDtaxa (pr2 V5) with dada2/phyloseq
DECIPHER taxonomyassignment phyloseq dada2 Pr2V5
updated 8 days ago by • 0 • written 11 weeks ago by • 0
2
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1
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1.9k
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Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq microbiome Software
updated 18 months ago by ★ 4.8k • written 18 months ago by ▴ 10
0
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0
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687
views
Try to understand better how to set out an effective sample size within the MetagenomSeq package in microbiome ?
Metagenomics metagenomeSeq microbiome phyloseq microbiomeDataSets
19 months ago Mohamed ▴ 30
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3
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1.4k
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Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 8 months ago by • 0 • written 22 months ago by • 0
2
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1
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4.7k
views
does anyone how to create rarefaction curves from a phyloseq object?
phyloseq Phylogenetics
updated 2.0 years ago by ▴ 20 • written 2.0 years ago by • 0
0
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3
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2.4k
views
I cannot install "microbiome"
GenomeInfoDbData microbiome phyloseq
updated 2.6 years ago by 700 • written 2.6 years ago by • 0
0
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1
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922
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error installing phyloseq
phyloseq
updated 2.8 years ago by 4.1k • written 2.8 years ago by • 0
0
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3
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1.2k
views
Controversial DESEQ2 results
phyloseq DESeq2
updated 2.8 years ago by 43k • written 2.8 years ago by • 0
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0
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703
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Association between ohylum and genus on microbiome data sets.
phyloseq
2.9 years ago Edmond • 0
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0
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1.8k
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How to pool phyloseq data?
phyloseq r
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
0
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4
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2.7k
views
Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings phyloseq
updated 3.0 years ago by 68k • written 3.0 years ago by • 0
0
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1
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1.1k
views
Deseq workflow for phyloseq object and complicated data structure?
phyloseq DESeq2
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
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4
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2.3k
views
Cannot install Phyloseq and dada2
GenomeInfoDbData phyloseq dada2
3.2 years ago ymtan • 0
0
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1
reply
942
views
Error in 'differential_abundance'
phyloseq devtools
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
0
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6
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1.7k
views
convert default phylip to sequential phylip
phyloseq Phylogenetics
updated 23 months ago by • 0 • written 3.6 years ago by • 0
0
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0
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1.1k
views
Construct a phyloseq object directly from the dada2 outputs
phyloseq dada2
3.6 years ago Manijeh • 0
0
votes
3
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1.4k
views
DESeq2: difficulty with contrasts and main effects
DESeq2 phyloseq contrasts
updated 3.6 years ago by ★ 4.0k • written 3.6 years ago by • 0
0
votes
5
replies
7.7k
views
Problems with installation of 'phyloseq
phyloseq
updated 3.7 years ago by ★ 4.0k • written 3.7 years ago by • 0
0
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0
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949
views
Construct Phylogenetic Tree
phyloseq
3.8 years ago klltnq • 0
0
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0
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775
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Code Issue
phyloseq
3.8 years ago klltnq • 0
0
votes
1
reply
904
views
Purpose of seqtabNoC
phyloseq
updated 3.8 years ago by ★ 4.0k • written 3.8 years ago by • 0
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3
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1.1k
views
Installing Packages repeatedly
phyloseq
updated 3.8 years ago by ★ 4.0k • written 3.8 years ago by • 0
0
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1
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2.8k
views
Import MetaPhlAn3 to Phyloseq
Metaphlan3 Metagenomics phyloseq
updated 3.8 years ago by ★ 1.1k • written 3.8 years ago by • 0
1
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1
reply
4.7k
views
Setting up bioconductor on a Linux server using conda
dada2 conda phyloseq
updated 4.0 years ago by 68k • written 4.0 years ago by • 0
1
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3
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1.4k
views
How to assign random effect factor in DESeq2 desing?
StatisticalMethod DESeq2 phyloseq
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
4
votes
3
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1.5k
views
Paired-test between two groups within a condition after phyloseq_to_deseq2
DESeq2 phyloseq
updated 4.1 years ago by 43k • written 4.1 years ago by ▴ 10
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0
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1.4k
views
Co-occurrence Network Analysis between Algae and Bacteria
igraph networkanalysis Phylogenetics phyloseq
4.2 years ago Chantel • 0
1
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2
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2.9k
views
Bioconductor install error
phyloseq Bioconductor
4.3 years ago Tess • 0
2
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2
replies
2.3k
views
Bioconductor phyloseq taking forever to install?
Bioconductor phyloseq
4.4 years ago garfield320 ▴ 30
0
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1
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1.5k
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Can I use pseudocounts for differential abundance of OTUs?
metagenomics deseq2 PHYLOSEQ
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
0
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2
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2.4k
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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
4.7 years ago jaiber.solano.i • 0
0
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3
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1.4k
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Nested design- phyloseq_to_deseq
deseq2 Phyloseq Nested
updated 5.0 years ago by 43k • written 5.0 years ago by • 0
0
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2
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3.4k
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 5.3 years ago by 25k • written 5.3 years ago by • 0
0
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0
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1.1k
views
Problems with creating phyloseq bar plots from a table with species data
phyloseq microbiome analysis
6.1 years ago lm795 ▴ 10
0
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2
replies
1.3k
views
Phyloseq to DESeq2
deseq2 phyloseq
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
0
votes
1
reply
1.9k
views
Import_biom with tree problem
phyloseq mothur 16s
6.4 years ago andrebolerbarros ▴ 20
5
votes
11
replies
3.2k
views
Error while installing Phyloseq using biocLite
bioclite phyloseq install error
6.5 years ago khp ▴ 30
0
votes
9
replies
2.9k
views
DESEQ2 / Phyloseq contrasts no longer work as before following update
deseq2 phyloseq
6.5 years ago eoin • 0
0
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1
reply
1.1k
views
Invalid class DESeqDataSet object with Phyloseq
deseq2 phyloseq
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 10
0
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1
reply
2.1k
views
Install package phyloseq
installation phyloseq
updated 7.0 years ago by 25k • written 7.0 years ago by • 0
0
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1
reply
2.0k
views
tip_glom and annotations?
ggtree treeio phyloseq annotation tip_glom
updated 7.1 years ago by ★ 1.2k • written 7.1 years ago by • 0
1
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1
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1.7k
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
1
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8
replies
6.9k
views
Cannot read Biom file
r biomformat phyloseq
updated 7.4 years ago by ★ 1.1k • written 7.4 years ago by • 0
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0
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1.6k
views
Problem with ade4 when upgrading to Rstudio 1.1 and OpenR 3.4
phyloseq installation ade4 macos
7.4 years ago sprague • 0
3
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2
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4.0k
views
DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
0
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1
reply
1.6k
views
phyloseq heatmap blank after multiple package updates
phyloseq heatmap
updated 7.6 years ago by ★ 13k • written 7.6 years ago by • 0
1
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3
replies
2.3k
views
Error bars on DESeq2 visuals
deseq2 metagenomics phyloseq ggplot2
7.6 years ago lauren.czaplicki • 0
0
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1
reply
1.9k
views
Phyloseq to DESeq2 with multiple variables
deseq2 phyloseq multiple time points
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
0
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0
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1.6k
views
Phylogenetic tree from marker genes
ape phyloseq dist metagenomics
7.9 years ago David ▴ 860
1
vote
1
reply
4.1k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
8.0 years ago stats134711 • 0
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Comment: Package developing and interoperation with Bioconductor by shepherl 4.1k
Using an example with SummarizedExperiment would satisfy the requirement; however the package should take the object directly and not just…
Comment: Error in H5Dclose(h5dataset) when trying to read in kallisto h5 files by Sofia • 0
1. I have tried to update the packages and R but to no avail. I keep getting either this error or : `Error in H5Fclose(file$H5Identifier) …
Comment: Validity of SingleR with very small bulk RNAseq reference by Rohit • 0
Hi @nhaus So, what did you end up doing in such a scenario? I am facing a similar challenge
Comment: CpGs with genomic positions greater than the chromosome size in EPICv2? by Joshua Llano • 0
Thank you for your reply James. I was worried that it was my mistake.
Comment: Annotation package for Manduca sexta by GA ▴ 10
Thank you!
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Answer: CpGs with genomic positions greater than the chromosome size in EPICv2?
Answer: Explannation for ROAST results
A: How DiffBind run PCA based on peak data?
Looking for equivalent EPIC chip v1 vs. v2 annotation variables
Properly constructing a hypergeometric test
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