Showing : Phyloseq • reset
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Phylogenetic tree from marker genes
ape phyloseq dist metagenomics
8.5 years ago David ▴ 860
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Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
8.5 years ago stats134711 • 0
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2.6k
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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 8.6 years ago by ★ 1.2k • written 8.6 years ago by • 0
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DESeq2 in phyloseq
deseq2 phyloseq
8.6 years ago sarahmacdonald86 • 0
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Controlling colours assigned to order in DeSeq2 plot in phyloseq
phyloseq color ggplot2
updated 8.7 years ago by 43k • written 8.7 years ago by • 0
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1.8k
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rlogTransformation vs getVarianceStabilizedData
deseq2 r phyloseq
updated 8.9 years ago by 43k • written 8.9 years ago by ▴ 10
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Error with phyloseq R package with Conda install
software error phyloseq anaconda
written 9.0 years ago by • 0
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2.5k
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phyloseq biom json format conversion needed to hdf5 format for qiime
biom json hdf5 qiime phyloseq
updated 9.0 years ago by ▴ 550 • written 9.0 years ago by • 0
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2.7k
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phyloseq merge_samples attempt to set rownames on an object with no dimensions
phyloseq merge_samples rownames error
9.1 years ago newmanss • 0
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1.9k
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DESeq2 blocking by condition over time
deseq2 phyloseq time course
9.2 years ago akp • 0
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displaying network from microbial count data
phyloseq
9.2 years ago chrisclarkson100 ▴ 50
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Testing for OTUs with negatively correlated abundances/occurrences
phyloseq
9.3 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 9.4 years ago by 43k • written 9.4 years ago by • 0
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1.3k
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Aditional undesired sample
phyloseq
9.6 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 9.6 years ago by ▴ 20 • written 9.6 years ago by ▴ 10
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2
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7.3k
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Interpretation of intercept-only model (~1) in DESeq2
deseq2 phyloseq
updated 9.7 years ago by 43k • written 9.7 years ago by ▴ 10
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6
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4.0k
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Alpha diversity on Rlogtransformed data
deseq2 phyloseq metagenomeseq
9.9 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 9.9 years ago by 43k • written 9.9 years ago by • 0
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1.7k
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phyloseq - plot_bar() error
phyloseq plot_bar()
updated 10.0 years ago by ▴ 20 • written 10.0 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 10.0 years ago by ▴ 20 • written 10.0 years ago by • 0
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10
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2.8k
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Multi-factor Comparison in DESeq 2 Issue
deseq2 phyloseq
updated 10.7 years ago by ★ 7.9k • written 10.7 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 10.8 years ago by ▴ 120
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1.8k
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Loading Phyloseq into R- R crashes
software error phyloseq R
10.8 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
11.3 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 11.3 years ago by 43k • written 11.3 years ago by ▴ 60
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Phyloseq/DEseq transformed data
DESeq phyloseq DESeq phyloseq
11.5 years ago Susan Holmes ▴ 120
76 results • Page 2 of 2
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Comment: Using DESeq2 for age prediction by ATpoint ★ 5.0k
You sure will find online tutorials on regression models / machine learning classifiers. The support site is for help with Bioconductor. Ch…
Comment: Using DESeq2 for age prediction by picasa1983 • 0
Thanks ! Do you have any idea how to do that ?
Answer: Using DESeq2 for age prediction by ATpoint ★ 5.0k
The package has no such inbuilt function but you are free to use the vst (or any normalized) counts to train a regression model or classifi…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
Votes
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
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