Showing : phyloseq • reset
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How can I correctly use phyloseq with Docker?
phylo phyloseq Docker
written 4 months ago by • 0
0
votes
1
reply
351
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DESeq2 from phyloseq error
DESeq2 phyloseq
3 months ago asafpr • 0
0
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2
replies
811
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Issue when attempting to use output from DECIPHER IDtaxa (pr2 V5) with dada2/phyloseq
DECIPHER taxonomyassignment phyloseq dada2 Pr2V5
updated 5 months ago by • 0 • written 7 months ago by • 0
0
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3
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1.7k
views
Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 13 months ago by • 0 • written 2.2 years ago by • 0
2
votes
1
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2.2k
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Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq microbiome Software
updated 23 months ago by ★ 4.9k • written 23 months ago by ▴ 10
0
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0
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780
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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
2.0 years ago Mohamed ▴ 30
0
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6
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1.8k
views
convert default phylip to sequential phylip
phyloseq Phylogenetics
updated 2.4 years ago by • 0 • written 4.0 years ago by • 0
2
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1
reply
5.3k
views
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 3.1 years ago by • 0
0
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1
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1.0k
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error installing phyloseq
phyloseq
updated 3.2 years ago by 4.2k • written 3.2 years ago by • 0
0
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3
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1.3k
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Controversial DESEQ2 results
phyloseq DESeq2
updated 3.2 years ago by 43k • written 3.3 years ago by • 0
0
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0
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810
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Association between ohylum and genus on microbiome data sets.
phyloseq
3.3 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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2.9k
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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 3.5 years ago by 68k • written 3.5 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 3.6 years ago by 43k • written 3.6 years ago by • 0
0
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4
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2.6k
views
Cannot install Phyloseq and dada2
GenomeInfoDbData phyloseq dada2
3.6 years ago ymtan • 0
0
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1
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1.0k
views
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
4.0 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 4.1 years ago by ★ 4.0k • written 4.1 years ago by • 0
0
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5
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8.1k
views
Problems with installation of 'phyloseq
phyloseq
updated 4.1 years ago by ★ 4.0k • written 4.1 years ago by • 0
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1
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1.0k
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Purpose of seqtabNoC
phyloseq
updated 4.2 years ago by ★ 4.0k • written 4.2 years ago by • 0
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0
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1.0k
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Construct Phylogenetic Tree
phyloseq
4.2 years ago klltnq • 0
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0
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841
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Code Issue
phyloseq
4.2 years ago klltnq • 0
0
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3
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1.2k
views
Installing Packages repeatedly
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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3.0k
views
Import MetaPhlAn3 to Phyloseq
Metaphlan3 Metagenomics phyloseq
updated 4.2 years ago by ★ 1.1k • written 4.2 years ago by • 0
1
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1
reply
5.3k
views
Setting up bioconductor on a Linux server using conda
dada2 conda phyloseq
updated 4.4 years ago by 68k • written 4.4 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 4.5 years ago by 43k • written 4.5 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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1.7k
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Co-occurrence Network Analysis between Algae and Bacteria
igraph networkanalysis Phylogenetics phyloseq
updated 5 months ago by • 0 • written 4.6 years ago by • 0
1
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2
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3.1k
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Bioconductor install error
phyloseq Bioconductor
4.8 years ago Tess • 0
2
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2
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2.6k
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Bioconductor phyloseq taking forever to install?
Bioconductor phyloseq
4.8 years ago garfield320 ▴ 30
0
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1
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1.6k
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Can I use pseudocounts for differential abundance of OTUs?
metagenomics deseq2 PHYLOSEQ
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
0
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2
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2.6k
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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
5.2 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 5.4 years ago by 43k • written 5.4 years ago by • 0
0
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2
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3.6k
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 5.7 years ago by 25k • written 5.7 years ago by • 0
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
views
Phyloseq to DESeq2
deseq2 phyloseq
updated 6.6 years ago by 43k • written 6.6 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
6.9 years ago andrebolerbarros ▴ 20
5
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11
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3.4k
views
Error while installing Phyloseq using biocLite
bioclite phyloseq install error
6.9 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
views
Invalid class DESeqDataSet object with Phyloseq
deseq2 phyloseq
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 10
0
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1
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2.3k
views
Install package phyloseq
installation phyloseq
updated 7.5 years ago by 25k • written 7.5 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 7.6 years ago by ★ 1.2k • written 7.6 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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7.2k
views
Cannot read Biom file
r biomformat phyloseq
updated 7.8 years ago by ★ 1.1k • written 7.8 years ago by • 0
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0
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1.7k
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Problem with ade4 when upgrading to Rstudio 1.1 and OpenR 3.4
phyloseq installation ade4 macos
7.9 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 8.0 years ago by 43k • written 8.0 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 8.0 years ago by ★ 13k • written 8.0 years ago by • 0
1
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3
replies
2.5k
views
Error bars on DESeq2 visuals
deseq2 metagenomics phyloseq ggplot2
8.0 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 8.1 years ago by 43k • written 8.1 years ago by • 0
76 results • Page 1 of 2
Recent ...
Replies
Answer: ROAST compare results with complex design by James W. MacDonald 68k
You are specifying that the last column of your design should be used as the contrast. You should instead use `contrast[,1]`, which will us…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Yes. You can infer that by figuring out what each coefficient measures. Here is your design matrix: ``` > targets ID Name phase G…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Not sure I understand. You ask how to do something and then show how one would do so.
Comment: DiffBind getting Fold values of near 0 by littlefishes20 ▴ 10
Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…
Votes
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Can NanoString data be analyzed using DESeq2?
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