Showing : phyloseq • reset
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Setting up bioconductor on a Linux server using conda
dada2 conda phyloseq
updated 11 weeks ago by 57k • written 11 weeks ago by • 0
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3
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156
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How to assign random effect factor in DESeq2 desing?
StatisticalMethod DESeq2 phyloseq
updated 3 months ago by 33k • written 3 months ago by • 0
4
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3
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186
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Paired-test between two groups within a condition after phyloseq_to_deseq2
DESeq2 phyloseq
updated 4 months ago by 33k • written 4 months ago by ▴ 10
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89
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Co-occurrence Network Analysis between Algae and Bacteria
igraph networkanalysis Phylogenetics phyloseq
5 months ago Chantel • 0
1
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2
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262
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Bioconductor install error
phyloseq Bioconductor
6 months ago Tess • 0
2
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2
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217
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Bioconductor phyloseq taking forever to install?
Bioconductor phyloseq
7 months ago garfield320 ▴ 30
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1
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191
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Can I use pseudocounts for differential abundance of OTUs?
metagenomics deseq2 PHYLOSEQ
updated 10 months ago by 33k • written 10 months ago by • 0
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2
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175
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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
11 months ago jaiber.solano.i • 0
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3
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129
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Nested design- phyloseq_to_deseq
deseq2 Phyloseq Nested
updated 14 months ago by 33k • written 14 months ago by • 0
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2
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820
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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 18 months ago by 25k • written 18 months ago by • 0
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222
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Problems with creating phyloseq bar plots from a table with species data
phyloseq microbiome analysis
2.3 years ago lm795 ▴ 10
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2
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374
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Phyloseq to DESeq2
deseq2 phyloseq
updated 2.4 years ago by 33k • written 2.4 years ago by • 0
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1
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503
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Import_biom with tree problem
phyloseq mothur 16s
2.6 years ago andrebolerbarros ▴ 10
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11
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1.4k
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Error while installing Phyloseq using biocLite
bioclite phyloseq install error
2.7 years ago khp ▴ 30
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9
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887
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DESEQ2 / Phyloseq contrasts no longer work as before following update
deseq2 phyloseq
2.7 years ago eoin • 0
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1
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352
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Invalid class DESeqDataSet object with Phyloseq
deseq2 phyloseq
updated 2.9 years ago by 33k • written 2.9 years ago by ▴ 10
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1
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647
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Install package phyloseq
installation phyloseq
updated 3.2 years ago by 25k • written 3.2 years ago by • 0
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1
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611
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tip_glom and annotations?
ggtree treeio phyloseq annotation tip_glom
updated 3.3 years ago by ★ 1.2k • written 3.3 years ago by • 0
1
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1
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630
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Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
updated 3.5 years ago by 33k • written 3.5 years ago by • 0
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8
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2.5k
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Cannot read Biom file
r biomformat phyloseq
updated 3.6 years ago by ▴ 980 • written 3.6 years ago by • 0
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483
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Problem with ade4 when upgrading to Rstudio 1.1 and OpenR 3.4
phyloseq installation ade4 macos
3.7 years ago sprague • 0
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2
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1.4k
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DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
updated 3.8 years ago by 33k • written 3.8 years ago by • 0
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1
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619
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phyloseq heatmap blank after multiple package updates
phyloseq heatmap
updated 3.8 years ago by 13k • written 3.8 years ago by • 0
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3
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876
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Error bars on DESeq2 visuals
deseq2 metagenomics phyloseq ggplot2
3.8 years ago lauren.czaplicki • 0
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718
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Phyloseq to DESeq2 with multiple variables
deseq2 phyloseq multiple time points
updated 3.9 years ago by 33k • written 3.9 years ago by • 0
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597
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Phylogenetic tree from marker genes
ape phyloseq dist metagenomics
4.1 years ago David ▴ 860
1
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1
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1.8k
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Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
4.2 years ago stats134711 • 0
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1.1k
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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 4.3 years ago by ★ 1.2k • written 4.3 years ago by • 0
2
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2
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804
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DESeq2 in phyloseq
deseq2 phyloseq
4.3 years ago sarahmacdonald86 • 0
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2
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965
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Controlling colours assigned to order in DeSeq2 plot in phyloseq
phyloseq color ggplot2
updated 4.3 years ago by 33k • written 4.3 years ago by • 0
1
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2
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781
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rlogTransformation vs getVarianceStabilizedData
deseq2 r phyloseq
updated 4.5 years ago by 33k • written 4.5 years ago by ▴ 10
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1.0k
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Error with phyloseq R package with Conda install
software error phyloseq anaconda
4.6 years ago kpitz23 • 0
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1.1k
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phyloseq biom json format conversion needed to hdf5 format for qiime
biom json hdf5 qiime phyloseq
updated 4.6 years ago by ▴ 540 • written 4.6 years ago by • 0
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1.2k
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phyloseq merge_samples attempt to set rownames on an object with no dimensions
phyloseq merge_samples rownames error
4.7 years ago newmanss • 0
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3
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879
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DESeq2 blocking by condition over time
deseq2 phyloseq time course
4.8 years ago akp • 0
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514
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displaying network from microbial count data
phyloseq
4.9 years ago chrisclarkson100 ▴ 50
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436
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Testing for OTUs with negatively correlated abundances/occurrences
phyloseq
4.9 years ago am39 • 0
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3
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1.3k
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Newer version of DESeq2 gives different results
deseq2 phyloseq
updated 5.0 years ago by 33k • written 5.0 years ago by • 0
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511
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Aditional undesired sample
phyloseq
5.2 years ago sanrrone • 0
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2
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1.5k
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DESEQ2 (R) design/contrast formula questions
deseq2 phyloseq multiple factor design paired samples
updated 5.2 years ago by ▴ 20 • written 5.2 years ago by ▴ 10
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3.4k
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Interpretation of intercept-only model (~1) in DESeq2
deseq2 phyloseq
updated 5.3 years ago by 33k • written 5.3 years ago by ▴ 10
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6
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1.7k
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Alpha diversity on Rlogtransformed data
deseq2 phyloseq metagenomeseq
5.5 years ago David ▴ 860
2
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1
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1.2k
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Using DESeq2 after agglomerating OTUs
phyloseq deseq2 estimatesizefactors
updated 5.5 years ago by 33k • written 5.5 years ago by • 0
0
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897
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phyloseq - plot_bar() error
phyloseq plot_bar()
updated 5.6 years ago by ▴ 20 • written 5.6 years ago by ▴ 120
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9
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15k
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Error in file(con, “r”) : cannot open the connection
r phyloseq import_biom otu qiime
updated 5.7 years ago by ▴ 20 • written 5.7 years ago by • 0
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10
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1.6k
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Multi-factor Comparison in DESeq 2 Issue
deseq2 phyloseq
updated 6.4 years ago by 7.6k • written 6.4 years ago by • 0
0
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1
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1.3k
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Phyloseq: How to add sample table to phyloseq object
phyloseq sample_table phyloseq
6.4 years ago Brian Smith ▴ 120
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1.1k
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Loading Phyloseq into R- R crashes
software error phyloseq R
6.4 years ago locon833 • 0
0
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1
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846
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DESeqs two-factor two-level, interaction is interested
Sequencing GO phyloseq DESeq2 Sequencing GO phyloseq DESeq2
7.0 years ago • updated 6.9 years ago Shucong Li ▴ 60
1
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2
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1.7k
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DESeqs two-factor two-level, interaction is interested
Sequencing GO phyloseq DESeq2 Sequencing GO phyloseq DESeq2
updated 7.0 years ago by 33k • written 7.0 years ago by ▴ 60
50 results • Page 1 of 1
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Answer: Seurat: normalized data in the integrated assay by Peter Hickey ▴ 460
Seurat is not a Bioconductor package. I suggest asking on their own discussion forum https://github.com/satijalab/seurat/discussions
Comment: matrix with Salmon gene-level quantifications in DESeq by Michael Love 33k
I feel like this is definitely covered in the vignette. We show importing multiple samples to gene level.
Comment: matrix with Salmon gene-level quantifications in DESeq by luca.s ▴ 10
Thanks James for the quick answer, but does the tximport package work also for importing a single matrix in which are contained all gene qu…
Comment: ORF finding in DECIPHER by Erik Wright ▴ 150
Thanks for reporting this issue. 1. Which version of DECIPHER are you using? 2.18 has known bugs but 2.20 should be fine. 2. Are your se…
Comment: DESeq2: Variable Importance by Michael Love 33k
What you do with the deviance is up to you, I was just pointing out that it is an outputted quantity.
Votes
Correct use of TMM / normalization factors based on large bins
Answer: How to do annotation with Limma
Final List of Deprecated Packages for Bioc3.13
Answer: RNAseq : identical sample-sample distances after using limma::removeBatchEffect
Answer: RNAseq : identical sample-sample distances after using limma::removeBatchEffect
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