Showing : phyloseq • reset
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31
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Association between ohylum and genus on microbiome data sets.
phyloseq
12 days ago Edmond • 0
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0
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94
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How to pool phyloseq data?
phyloseq r
updated 8 weeks ago by 36k • written 8 weeks ago by • 0
0
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4
replies
203
views
Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings phyloseq
updated 9 weeks ago by 59k • written 9 weeks ago by • 0
0
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1
reply
166
views
Deseq workflow for phyloseq object and complicated data structure?
phyloseq DESeq2
updated 3 months ago by 36k • written 4 months ago by • 0
0
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4
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349
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Cannot install Phyloseq and dada2
GenomeInfoDbData phyloseq dada2
4 months ago • updated 3 months ago ymtan • 0
0
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1
reply
145
views
Error in 'differential_abundance'
phyloseq devtools
updated 4 months ago by 36k • written 4 months ago by • 0
0
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1
reply
250
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convert default phylip to sequential phylip
phyloseq Phylogenetics
updated 4 months ago by • 0 • written 8 months ago by • 0
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0
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203
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Construct a phyloseq object directly from the dada2 outputs
phyloseq dada2
9 months ago Manijeh • 0
0
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3
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258
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DESeq2: difficulty with contrasts and main effects
DESeq2 phyloseq contrasts
updated 9 months ago by 3.5k • written 9 months ago by • 0
0
votes
5
replies
1.8k
views
Problems with installation of 'phyloseq
phyloseq
updated 9 months ago by 3.5k • written 9 months ago by • 0
0
votes
1
reply
205
views
Purpose of seqtabNoC
phyloseq
updated 10 months ago by 3.5k • written 10 months ago by • 0
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0
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183
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Construct Phylogenetic Tree
phyloseq
10 months ago klltnq • 0
0
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0
replies
176
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Code Issue
phyloseq
10 months ago klltnq • 0
0
votes
3
replies
242
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Installing Packages repeatedly
phyloseq
updated 10 months ago by 3.5k • written 10 months ago by • 0
0
votes
1
reply
655
views
Import MetaPhlAn3 to Phyloseq
Metaphlan3 Metagenomics phyloseq
updated 10 months ago by 1.1k • written 10 months ago by • 0
1
vote
1
reply
1.1k
views
Setting up bioconductor on a Linux server using conda
dada2 conda phyloseq
updated 13 months ago by 59k • written 13 months ago by • 0
1
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3
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341
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How to assign random effect factor in DESeq2 desing?
StatisticalMethod DESeq2 phyloseq
updated 15 months ago by 36k • written 15 months ago by • 0
4
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3
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413
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Paired-test between two groups within a condition after phyloseq_to_deseq2
DESeq2 phyloseq
updated 15 months ago by 36k • written 15 months ago by ▴ 10
0
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0
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398
views
Co-occurrence Network Analysis between Algae and Bacteria
igraph networkanalysis Phylogenetics phyloseq
16 months ago Chantel • 0
1
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2
replies
1.1k
views
Bioconductor install error
phyloseq Bioconductor
18 months ago Tess • 0
2
votes
2
replies
566
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Bioconductor phyloseq taking forever to install?
Bioconductor phyloseq
18 months ago garfield320 ▴ 30
0
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1
reply
537
views
Can I use pseudocounts for differential abundance of OTUs?
metagenomics deseq2 PHYLOSEQ
updated 21 months ago by 36k • written 21 months ago by • 0
0
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2
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418
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
22 months ago jaiber.solano.i • 0
0
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3
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357
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Nested design- phyloseq_to_deseq
deseq2 Phyloseq Nested
updated 2.1 years ago by 36k • written 2.1 years ago by • 0
0
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2
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1.8k
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 2.4 years ago by 25k • written 2.4 years ago by • 0
0
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0
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383
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Problems with creating phyloseq bar plots from a table with species data
phyloseq microbiome analysis
3.3 years ago lm795 ▴ 10
0
votes
2
replies
497
views
Phyloseq to DESeq2
deseq2 phyloseq
updated 3.3 years ago by 36k • written 3.3 years ago by • 0
0
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1
reply
786
views
Import_biom with tree problem
phyloseq mothur 16s
3.6 years ago andrebolerbarros ▴ 10
5
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11
replies
1.8k
views
Error while installing Phyloseq using biocLite
bioclite phyloseq install error
3.6 years ago khp ▴ 30
0
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9
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1.2k
views
DESEQ2 / Phyloseq contrasts no longer work as before following update
deseq2 phyloseq
3.7 years ago eoin • 0
0
votes
1
reply
445
views
Invalid class DESeqDataSet object with Phyloseq
deseq2 phyloseq
updated 3.8 years ago by 36k • written 3.8 years ago by ▴ 10
0
votes
1
reply
834
views
Install package phyloseq
installation phyloseq
updated 4.2 years ago by 25k • written 4.2 years ago by • 0
0
votes
1
reply
795
views
tip_glom and annotations?
ggtree treeio phyloseq annotation tip_glom
updated 4.3 years ago by ★ 1.2k • written 4.3 years ago by • 0
1
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1
reply
811
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
updated 4.5 years ago by 36k • written 4.5 years ago by • 0
1
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8
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3.4k
views
Cannot read Biom file
r biomformat phyloseq
updated 4.5 years ago by ▴ 990 • written 4.5 years ago by • 0
0
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0
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624
views
Problem with ade4 when upgrading to Rstudio 1.1 and OpenR 3.4
phyloseq installation ade4 macos
4.6 years ago sprague • 0
2
votes
2
replies
1.9k
views
DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
updated 4.7 years ago by 36k • written 4.7 years ago by • 0
0
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1
reply
748
views
phyloseq heatmap blank after multiple package updates
phyloseq heatmap
updated 4.7 years ago by 13k • written 4.7 years ago by • 0
1
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3
replies
1.1k
views
Error bars on DESeq2 visuals
deseq2 metagenomics phyloseq ggplot2
4.7 years ago lauren.czaplicki • 0
0
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1
reply
913
views
Phyloseq to DESeq2 with multiple variables
deseq2 phyloseq multiple time points
updated 4.8 years ago by 36k • written 4.8 years ago by • 0
0
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0
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752
views
Phylogenetic tree from marker genes
ape phyloseq dist metagenomics
5.1 years ago David ▴ 860
1
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1
reply
2.2k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
5.1 years ago stats134711 • 0
0
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1
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1.4k
views
ggtree facet_plot question using geom_boxplot to plot abundance data corresponding to tree tips
ggtree ggplot2 phyloseq geom_boxplot facet_plot
updated 5.2 years ago by ★ 1.2k • written 5.2 years ago by • 0
2
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2
replies
1.0k
views
DESeq2 in phyloseq
deseq2 phyloseq
5.2 years ago sarahmacdonald86 • 0
0
votes
2
replies
1.2k
views
Controlling colours assigned to order in DeSeq2 plot in phyloseq
phyloseq color ggplot2
updated 5.2 years ago by 36k • written 5.2 years ago by • 0
1
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2
replies
944
views
rlogTransformation vs getVarianceStabilizedData
deseq2 r phyloseq
updated 5.5 years ago by 36k • written 5.5 years ago by ▴ 10
0
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0
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1.4k
views
Error with phyloseq R package with Conda install
software error phyloseq anaconda
5.5 years ago kpitz23 • 0
0
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1
reply
1.3k
views
phyloseq biom json format conversion needed to hdf5 format for qiime
biom json hdf5 qiime phyloseq
updated 5.5 years ago by ▴ 550 • written 5.6 years ago by • 0
0
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1
reply
1.5k
views
phyloseq merge_samples attempt to set rownames on an object with no dimensions
phyloseq merge_samples rownames error
5.6 years ago newmanss • 0
0
votes
3
replies
1.1k
views
DESeq2 blocking by condition over time
deseq2 phyloseq time course
5.7 years ago akp • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: TPM data Differential expression analysis by hnthirim ▴ 10
Hi @gordonsmyth, Question on your above answer: I have logTPM normalized data. Can I perform DE analysis using it on EdgeR, instead of in…
Comment: rtracklayer S.h by gibran • 0
Thanks, much appreciated. So I think this approach actually gets binaries and I'm not sure how to isolate the problem I was experiencing as…
Comment: DESeq2, Calculate the size factor by using median-of-ratio by KEREN • 0
Hi Michael, thank you for you reply. My concern here mainly focus on the high variances in samples of condition "mESC_mRNA_WT". I observed…
Comment: DiffBind: 0 consensus peaks for dba.peakset: New bug / undocumented change intro by Rory Stark ★ 4.4k
I agree the documentation could be clearer -- it took me a while to understand what it said so I could address your issue!
Answer: DiffBind: 0 consensus peaks for dba.peakset: New bug / undocumented change intro by chrarnold • 0
Thanks a lot for your quick reply, it is very appreciated! Indeed, with your 2 suggested modifications, I can again reproduce the results f…
Votes
Answer: rtracklayer S.h
Answer: rtracklayer S.h
Answer: DESeq2: Extracting Averaged Counts Information from dds and rld
Answer: DESeq2: Extracting Averaged Counts Information from dds and rld
Answer: DESeq2: Extracting Averaged Counts Information from dds and rld
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