Showing : phyloseq • reset
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Phylogenetic tree from marker genes
ape phyloseq dist metagenomics
8.4 years ago David ▴ 860
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4.3k
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Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
8.4 years ago stats134711 • 0
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ggtree facet_plot question using geom_boxplot to plot abundance data corresponding to tree tips
ggtree ggplot2 phyloseq geom_boxplot facet_plot
updated 8.5 years ago by ★ 1.2k • written 8.5 years ago by • 0
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DESeq2 in phyloseq
deseq2 phyloseq
8.5 years ago sarahmacdonald86 • 0
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2.3k
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Controlling colours assigned to order in DeSeq2 plot in phyloseq
phyloseq color ggplot2
updated 8.5 years ago by 43k • written 8.5 years ago by • 0
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1.8k
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rlogTransformation vs getVarianceStabilizedData
deseq2 r phyloseq
updated 8.8 years ago by 43k • written 8.8 years ago by ▴ 10
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2.6k
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Error with phyloseq R package with Conda install
software error phyloseq anaconda
written 8.8 years ago by • 0
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2.4k
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phyloseq biom json format conversion needed to hdf5 format for qiime
biom json hdf5 qiime phyloseq
updated 8.8 years ago by ▴ 550 • written 8.9 years ago by • 0
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2.6k
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phyloseq merge_samples attempt to set rownames on an object with no dimensions
phyloseq merge_samples rownames error
8.9 years ago newmanss • 0
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1.9k
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DESeq2 blocking by condition over time
deseq2 phyloseq time course
9.0 years ago akp • 0
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displaying network from microbial count data
phyloseq
9.1 years ago chrisclarkson100 ▴ 50
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Testing for OTUs with negatively correlated abundances/occurrences
phyloseq
9.1 years ago am39 • 0
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3
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2.4k
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Newer version of DESeq2 gives different results
deseq2 phyloseq
updated 9.2 years ago by 43k • written 9.2 years ago by • 0
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1.2k
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Aditional undesired sample
phyloseq
9.4 years ago sanrrone • 0
3
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2.5k
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DESEQ2 (R) design/contrast formula questions
deseq2 phyloseq multiple factor design paired samples
updated 9.4 years ago by ▴ 20 • written 9.4 years ago by ▴ 10
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2
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7.2k
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Interpretation of intercept-only model (~1) in DESeq2
deseq2 phyloseq
updated 9.5 years ago by 43k • written 9.5 years ago by ▴ 10
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6
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3.9k
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Alpha diversity on Rlogtransformed data
deseq2 phyloseq metagenomeseq
9.7 years ago David ▴ 860
2
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1
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2.2k
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Using DESeq2 after agglomerating OTUs
phyloseq deseq2 estimatesizefactors
updated 9.8 years ago by 43k • written 9.8 years ago by • 0
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1.6k
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phyloseq - plot_bar() error
phyloseq plot_bar()
updated 9.8 years ago by ▴ 20 • written 9.8 years ago by ▴ 120
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9
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21k
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Error in file(con, “r”) : cannot open the connection
r phyloseq import_biom otu qiime
updated 9.9 years ago by ▴ 20 • written 9.9 years ago by • 0
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10
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2.7k
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Multi-factor Comparison in DESeq 2 Issue
deseq2 phyloseq
updated 10.6 years ago by ★ 7.9k • written 10.6 years ago by • 0
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3
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5.7k
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Phyloseq: How to add sample table to phyloseq object
phyloseq sample_table phyloseq
written 10.6 years ago by ▴ 120
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1.7k
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Loading Phyloseq into R- R crashes
software error phyloseq R
10.7 years ago locon833 • 0
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1
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1.6k
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DESeqs two-factor two-level, interaction is interested
Sequencing GO phyloseq DESeq2 Sequencing GO phyloseq DESeq2
11.2 years ago Shucong Li ▴ 60
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2.4k
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DESeqs two-factor two-level, interaction is interested
Sequencing GO phyloseq DESeq2 Sequencing GO phyloseq DESeq2
updated 11.2 years ago by 43k • written 11.2 years ago by ▴ 60
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1.3k
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Phyloseq/DEseq transformed data
DESeq phyloseq DESeq phyloseq
11.4 years ago Susan Holmes ▴ 120
76 results • Page 2 of 2
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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…
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Answer: ROAST compare results with complex design
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
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