Showing : PHYLOSEQ • reset
2
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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 9.5 years ago by ▴ 20 • written 9.5 years ago by • 0
0
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5
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7.8k
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Problems with installation of 'phyloseq
phyloseq
updated 3.7 years ago by ★ 4.0k • written 3.7 years ago by • 0
2
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2
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7.0k
views
Interpretation of intercept-only model (~1) in DESeq2
deseq2 phyloseq
updated 9.1 years ago by 43k • written 9.1 years ago by ▴ 10
1
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8
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7.0k
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Cannot read Biom file
r biomformat phyloseq
updated 7.5 years ago by ★ 1.1k • written 7.5 years ago by • 0
0
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2
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5.4k
views
Phyloseq: How to add sample table to phyloseq object
phyloseq sample_table phyloseq
updated 21 days ago by • 0 • written 10.3 years ago by ▴ 120
2
votes
1
reply
4.9k
views
does anyone how to create rarefaction curves from a phyloseq object?
phyloseq Phylogenetics
updated 2.1 years ago by ▴ 20 • written 2.1 years ago by • 0
1
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1
reply
4.8k
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Setting up bioconductor on a Linux server using conda
dada2 conda phyloseq
updated 4.1 years ago by 68k • written 4.1 years ago by • 0
1
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1
reply
4.2k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
8.0 years ago stats134711 • 0
3
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2
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4.0k
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DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
0
votes
6
replies
3.7k
views
Alpha diversity on Rlogtransformed data
deseq2 phyloseq metagenomeseq
9.4 years ago David ▴ 860
0
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2
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3.4k
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 5.3 years ago by 25k • written 5.3 years ago by • 0
5
votes
11
replies
3.2k
views
Error while installing Phyloseq using biocLite
bioclite phyloseq install error
6.5 years ago khp ▴ 30
1
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2
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3.0k
views
Bioconductor install error
phyloseq Bioconductor
4.4 years ago Tess • 0
0
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9
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3.0k
views
DESEQ2 / Phyloseq contrasts no longer work as before following update
deseq2 phyloseq
6.6 years ago eoin • 0
0
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1
reply
2.8k
views
Import MetaPhlAn3 to Phyloseq
Metaphlan3 Metagenomics phyloseq
updated 3.8 years ago by ★ 1.1k • written 3.8 years ago by • 0
0
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4
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2.7k
views
Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings phyloseq
updated 3.1 years ago by 68k • written 3.1 years ago by • 0
1
vote
10
replies
2.5k
views
Multi-factor Comparison in DESeq 2 Issue
deseq2 phyloseq
updated 10.2 years ago by ★ 7.9k • written 10.2 years ago by • 0
0
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1
reply
2.5k
views
phyloseq merge_samples attempt to set rownames on an object with no dimensions
phyloseq merge_samples rownames error
8.6 years ago newmanss • 0
0
votes
2
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2.5k
views
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
4.8 years ago jaiber.solano.i • 0
0
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1
reply
2.5k
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Error with phyloseq R package with Conda install
software error phyloseq anaconda
written 8.5 years ago by • 0
0
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1
reply
2.4k
views
ggtree facet_plot question using geom_boxplot to plot abundance data corresponding to tree tips
ggtree ggplot2 phyloseq geom_boxplot facet_plot
updated 8.1 years ago by ★ 1.2k • written 8.1 years ago by • 0
0
votes
3
replies
2.4k
views
I cannot install "microbiome"
GenomeInfoDbData microbiome phyloseq
updated 2.7 years ago by 700 • written 2.7 years ago by • 0
3
votes
2
replies
2.4k
views
DESEQ2 (R) design/contrast formula questions
deseq2 phyloseq multiple factor design paired samples
updated 9.1 years ago by ▴ 20 • written 9.1 years ago by ▴ 10
0
votes
4
replies
2.4k
views
Cannot install Phyloseq and dada2
GenomeInfoDbData phyloseq dada2
3.3 years ago ymtan • 0
2
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2
replies
2.4k
views
Bioconductor phyloseq taking forever to install?
Bioconductor phyloseq
4.5 years ago garfield320 ▴ 30
1
vote
3
replies
2.3k
views
Error bars on DESeq2 visuals
deseq2 metagenomics phyloseq ggplot2
7.7 years ago lauren.czaplicki • 0
1
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2
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2.3k
views
DESeqs two-factor two-level, interaction is interested
Sequencing GO phyloseq DESeq2 Sequencing GO phyloseq DESeq2
updated 10.8 years ago by 43k • written 10.8 years ago by ▴ 60
0
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3
replies
2.3k
views
Newer version of DESeq2 gives different results
deseq2 phyloseq
updated 8.9 years ago by 43k • written 8.9 years ago by • 0
0
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1
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2.3k
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phyloseq biom json format conversion needed to hdf5 format for qiime
biom json hdf5 qiime phyloseq
updated 8.5 years ago by ▴ 550 • written 8.5 years ago by • 0
0
votes
2
replies
2.3k
views
Controlling colours assigned to order in DeSeq2 plot in phyloseq
phyloseq color ggplot2
updated 8.1 years ago by 43k • written 8.1 years ago by • 0
0
votes
1
reply
2.2k
views
Install package phyloseq
installation phyloseq
updated 7.1 years ago by 25k • written 7.1 years ago by • 0
2
votes
1
reply
2.2k
views
Using DESeq2 after agglomerating OTUs
phyloseq deseq2 estimatesizefactors
updated 9.4 years ago by 43k • written 9.4 years ago by • 0
0
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1
reply
2.0k
views
tip_glom and annotations?
ggtree treeio phyloseq annotation tip_glom
updated 7.2 years ago by ★ 1.2k • written 7.2 years ago by • 0
2
votes
1
reply
2.0k
views
Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq microbiome Software
updated 19 months ago by ★ 4.8k • written 19 months ago by ▴ 10
0
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1
reply
1.9k
views
Import_biom with tree problem
phyloseq mothur 16s
6.5 years ago andrebolerbarros ▴ 20
0
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1
reply
1.9k
views
Phyloseq to DESeq2 with multiple variables
deseq2 phyloseq multiple time points
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
0
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0
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1.9k
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How to pool phyloseq data?
phyloseq r
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
0
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3
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1.8k
views
DESeq2 blocking by condition over time
deseq2 phyloseq time course
8.6 years ago akp • 0
2
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2
replies
1.8k
views
DESeq2 in phyloseq
deseq2 phyloseq
8.1 years ago sarahmacdonald86 • 0
1
vote
2
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1.7k
views
rlogTransformation vs getVarianceStabilizedData
deseq2 r phyloseq
updated 8.4 years ago by 43k • written 8.4 years ago by ▴ 10
0
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6
replies
1.7k
views
convert default phylip to sequential phylip
phyloseq Phylogenetics
updated 24 months ago by • 0 • written 3.7 years ago by • 0
0
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0
replies
1.7k
views
Loading Phyloseq into R- R crashes
software error phyloseq R
10.3 years ago locon833 • 0
1
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1
reply
1.7k
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
0
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1
reply
1.7k
views
phyloseq heatmap blank after multiple package updates
phyloseq heatmap
updated 7.6 years ago by ★ 13k • written 7.6 years ago by • 0
0
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0
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1.6k
views
Problem with ade4 when upgrading to Rstudio 1.1 and OpenR 3.4
phyloseq installation ade4 macos
7.5 years ago sprague • 0
0
votes
1
reply
1.6k
views
Co-occurrence Network Analysis between Algae and Bacteria
igraph networkanalysis Phylogenetics phyloseq
updated 21 days ago by • 0 • written 4.3 years ago by • 0
0
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0
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1.6k
views
Phylogenetic tree from marker genes
ape phyloseq dist metagenomics
8.0 years ago David ▴ 860
0
votes
1
reply
1.6k
views
phyloseq - plot_bar() error
phyloseq plot_bar()
updated 9.5 years ago by ▴ 20 • written 9.5 years ago by ▴ 120
0
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1
reply
1.5k
views
Can I use pseudocounts for differential abundance of OTUs?
metagenomics deseq2 PHYLOSEQ
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
0
votes
1
reply
1.5k
views
DESeqs two-factor two-level, interaction is interested
Sequencing GO phyloseq DESeq2 Sequencing GO phyloseq DESeq2
10.8 years ago Shucong Li ▴ 60
50 results • Page 1 of 1
Recent ...
Replies
Comment: CluserProfiler message "No gene can be mapped" by Carolina • 0
There is, the overlap that reads out is ( Genes in common: 368 of 368 ). Here is the link for [background genes][1], [term2gene][2], [term2…
Comment: Differing results with DESeq2 by JKim • 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…
Answer: RNA-seq input to GRaNIE by James W. MacDonald 68k
This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…
Answer: Help using reduceSimMatrix with a custom annotation by sergisayolspuig ▴ 80
Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…
Votes
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
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