Showing : phyloseq • reset
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Co-occurrence Network Analysis between Algae and Bacteria
igraph networkanalysis Phylogenetics phyloseq
9 days ago Chantel • 0
1
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2
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100
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Bioconductor install error
phyloseq Bioconductor
8 weeks ago Tess • 0
2
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2
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89
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Bioconductor phyloseq taking forever to install?
Bioconductor phyloseq
11 weeks ago garfield320 • 30
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1
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98
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Can I use pseudocounts for differential abundance of OTUs?
metagenomics deseq2 PHYLOSEQ
5 months ago dc • 0 • updated 5 months ago Michael Love 31k
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2
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86
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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
6 months ago jaiber.solano.i • 0
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59
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Nested design- phyloseq_to_deseq
deseq2 Phyloseq Nested
9 months ago mpuli011 • 0 • updated 9 months ago Michael Love 31k
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2
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548
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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
13 months ago crgarcia • 0 • updated 13 months ago Martin Morgan 25k
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163
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Problems with creating phyloseq bar plots from a table with species data
phyloseq microbiome analysis
23 months ago lm795 • 0
0
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2
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319
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Phyloseq to DESeq2
deseq2 phyloseq
24 months ago staffordvigors • 0 • updated 24 months ago Michael Love 31k
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1
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371
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Import_biom with tree problem
phyloseq mothur 16s
2.2 years ago andrebolerbarros • 10
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11
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1.3k
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Error while installing Phyloseq using biocLite
bioclite phyloseq install error
2.3 years ago khp • 30
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9
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727
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DESEQ2 / Phyloseq contrasts no longer work as before following update
deseq2 phyloseq
2.3 years ago eoin • 0
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1
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305
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Invalid class DESeqDataSet object with Phyloseq
deseq2 phyloseq
2.4 years ago amgodogma • 10 • updated 2.4 years ago Michael Love 31k
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1
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575
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Install package phyloseq
installation phyloseq
2.8 years ago layeb • 0 • updated 2.8 years ago Martin Morgan 25k
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1
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535
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tip_glom and annotations?
ggtree treeio phyloseq annotation tip_glom
2.9 years ago werdnus • 0 • updated 2.9 years ago Guangchuang Yu ♦ 1.2k
1
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1
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543
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Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
3.1 years ago ssingh59 • 0 • updated 3.1 years ago Michael Love 31k
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8
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2.2k
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Cannot read Biom file
r biomformat phyloseq
3.2 years ago channen1221 • 0 • updated 3.2 years ago Axel Klenk • 940
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419
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Problem with ade4 when upgrading to Rstudio 1.1 and OpenR 3.4
phyloseq installation ade4 macos
3.3 years ago sprague • 0
2
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2
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1.2k
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DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
3.4 years ago couchc • 0 • updated 3.4 years ago Michael Love 31k
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1
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572
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phyloseq heatmap blank after multiple package updates
phyloseq heatmap
3.4 years ago newmanss • 0 • updated 3.4 years ago Wolfgang Huber 13k
1
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3
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791
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Error bars on DESeq2 visuals
deseq2 metagenomics phyloseq ggplot2
3.4 years ago lauren.czaplicki • 0
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1
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620
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Phyloseq to DESeq2 with multiple variables
deseq2 phyloseq multiple time points
3.5 years ago campbell87 • 0 • updated 3.5 years ago Michael Love 31k
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0
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539
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Phylogenetic tree from marker genes
ape phyloseq dist metagenomics
3.7 years ago David • 860
1
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1
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1.6k
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Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
3.8 years ago stats134711 • 0
0
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1
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1.0k
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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
3.9 years ago matthew.wipperman • 0 • updated 3.9 years ago Guangchuang Yu ♦ 1.2k
2
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2
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748
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DESeq2 in phyloseq
deseq2 phyloseq
3.9 years ago sarahmacdonald86 • 0
0
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2
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876
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Controlling colours assigned to order in DeSeq2 plot in phyloseq
phyloseq color ggplot2
3.9 years ago sarahmacdonald86 • 0 • updated 3.9 years ago Michael Love 31k
1
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2
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697
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rlogTransformation vs getVarianceStabilizedData
deseq2 r phyloseq
4.1 years ago fabian.roger08 • 10 • updated 4.1 years ago Michael Love 31k
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0
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945
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Error with phyloseq R package with Conda install
software error phyloseq anaconda
4.2 years ago kpitz23 • 0
0
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1
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993
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phyloseq biom json format conversion needed to hdf5 format for qiime
biom json hdf5 qiime phyloseq
4.2 years ago newmanss • 0 • updated 4.2 years ago Bernd Fischer • 540
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1.1k
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phyloseq merge_samples attempt to set rownames on an object with no dimensions
phyloseq merge_samples rownames error
4.3 years ago newmanss • 0
0
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3
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823
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DESeq2 blocking by condition over time
deseq2 phyloseq time course
4.4 years ago akp • 0
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0
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474
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displaying network from microbial count data
phyloseq
4.5 years ago chrisclarkson100 • 50
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392
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Testing for OTUs with negatively correlated abundances/occurrences
phyloseq
4.5 years ago am39 • 0
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3
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1.2k
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Newer version of DESeq2 gives different results
deseq2 phyloseq
4.6 years ago am39 • 0 • updated 4.6 years ago Michael Love 31k
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1
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454
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Aditional undesired sample
phyloseq
4.8 years ago sanrrone • 0
3
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2
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1.4k
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DESEQ2 (R) design/contrast formula questions
deseq2 phyloseq multiple factor design paired samples
4.8 years ago pete_bioinfo • 10 • updated 4.8 years ago mcmurdie • 20
1
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2
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3.1k
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Interpretation of intercept-only model (~1) in DESeq2
deseq2 phyloseq
4.9 years ago piensaglobalmente • 10 • updated 4.9 years ago Michael Love 31k
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6
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1.5k
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Alpha diversity on Rlogtransformed data
deseq2 phyloseq metagenomeseq
5.1 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
5.1 years ago brandilyn.peters • 0 • updated 5.1 years ago Michael Love 31k
0
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1
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840
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phyloseq - plot_bar() error
phyloseq plot_bar()
5.2 years ago Brian Smith • 120 • updated 5.2 years ago mcmurdie • 20
2
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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
5.3 years ago moanam • 0 • updated 5.3 years ago mcmurdie • 20
1
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10
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1.5k
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Multi-factor Comparison in DESeq 2 Issue
deseq2 phyloseq
6.0 years ago locon833 • 0 • updated 6.0 years ago Ryan C. Thompson 7.6k
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1
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1.1k
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Phyloseq: How to add sample table to phyloseq object
phyloseq sample_table phyloseq
6.0 years ago Brian Smith • 120
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0
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1.0k
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Loading Phyloseq into R- R crashes
software error phyloseq R
6.0 years ago locon833 • 0
0
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1
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691
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DESeqs two-factor two-level, interaction is interested
Sequencing GO phyloseq DESeq2 Sequencing GO phyloseq DESeq2
6.6 years ago • updated 6.5 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
6.6 years ago Shucong Li • 60 • updated 6.6 years ago Michael Love 31k
0
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0
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762
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Phyloseq/DEseq transformed data
DESeq phyloseq DESeq phyloseq
6.8 years ago Susan Holmes • 120
48 results • Page 1 of 1
Recent ...
Replies
Comment: How to use EnrichGo of Cluster Profiler by Lluís Revilla Sancho • 610
Could you share what is the output of `head(gene)`?
Comment: DESeq2 Error: ncol(countData) == nrow(colData) is not TRUE by Pedram • 0
Hello Michael I could not make the same matrix although I did what you said
Comment: Replace a specific nucleotide sequence, at a specific position, with another in by Konstantinos Yeles • 40
Hello @Benjamin-24571 for your example, I can suggest you this code: Read <- c("1","2","3","4") Sequences <- c("ACACCCACG", "AA…
Comment: CHIP Seq Analysis by DiffBind Package by shrinka.genetics • 0
Hello Thanks for your reply. I changed my file format and now it ran. It gave one plot also. All file s are in same directory. No…
Answer: Installing Bioconductor packages in Docker by Konstantinos Yeles • 40
Hello, @adklts-21974 My way to do the installation of packages in a docker is like this: FROM bioconductor/bioconductor_docker…
Votes
A: Interpreting the results from lfcShrink() with apeglm in DESeq2
A: single-cells RNA-seq analysis by MAST with unbalanced group size
single-cells RNA-seq analysis by MAST with unbalanced group size
A: single-cells RNA-seq analysis by MAST with unbalanced group size
A: DESeq2 1.20.0 lfcshrink function
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