Showing : Phyloseq • reset
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Issue when attempting to use output from DECIPHER IDtaxa (pr2 V5) with dada2/phyloseq
DECIPHER taxonomyassignment phyloseq dada2 Pr2V5
updated 5 days ago by • 0 • written 10 weeks ago by • 0
0
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3
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1.4k
views
Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 8 months ago by • 0 • written 21 months ago by • 0
2
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1
reply
1.9k
views
Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq microbiome Software
updated 18 months ago by ★ 4.7k • written 18 months ago by ▴ 10
0
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0
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687
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Try to understand better how to set out an effective sample size within the MetagenomSeq package in microbiome ?
Metagenomics metagenomeSeq microbiome phyloseq microbiomeDataSets
19 months ago Mohamed ▴ 30
0
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6
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1.7k
views
convert default phylip to sequential phylip
phyloseq Phylogenetics
updated 23 months ago by • 0 • written 3.6 years ago by • 0
2
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1
reply
4.7k
views
does anyone how to create rarefaction curves from a phyloseq object?
phyloseq Phylogenetics
updated 2.0 years ago by ▴ 20 • written 2.0 years ago by • 0
0
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3
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2.4k
views
I cannot install "microbiome"
GenomeInfoDbData microbiome phyloseq
updated 2.6 years ago by 700 • written 2.6 years ago by • 0
0
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1
reply
920
views
error installing phyloseq
phyloseq
updated 2.8 years ago by 4.1k • written 2.8 years ago by • 0
0
votes
3
replies
1.2k
views
Controversial DESEQ2 results
phyloseq DESeq2
updated 2.8 years ago by 43k • written 2.8 years ago by • 0
0
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0
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702
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Association between ohylum and genus on microbiome data sets.
phyloseq
2.9 years ago Edmond • 0
0
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0
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1.8k
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How to pool phyloseq data?
phyloseq r
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
0
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4
replies
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 3.0 years ago by 68k • written 3.0 years ago by • 0
0
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1
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1.1k
views
Deseq workflow for phyloseq object and complicated data structure?
phyloseq DESeq2
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
0
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4
replies
2.3k
views
Cannot install Phyloseq and dada2
GenomeInfoDbData phyloseq dada2
3.2 years ago ymtan • 0
0
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1
reply
940
views
Error in 'differential_abundance'
phyloseq devtools
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
0
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0
replies
1.0k
views
Construct a phyloseq object directly from the dada2 outputs
phyloseq dada2
3.6 years ago Manijeh • 0
0
votes
3
replies
1.4k
views
DESeq2: difficulty with contrasts and main effects
DESeq2 phyloseq contrasts
updated 3.6 years ago by ★ 4.0k • written 3.6 years ago by • 0
0
votes
5
replies
7.7k
views
Problems with installation of 'phyloseq
phyloseq
updated 3.6 years ago by ★ 4.0k • written 3.6 years ago by • 0
0
votes
1
reply
903
views
Purpose of seqtabNoC
phyloseq
updated 3.7 years ago by ★ 4.0k • written 3.7 years ago by • 0
0
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0
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947
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Construct Phylogenetic Tree
phyloseq
3.7 years ago klltnq • 0
0
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0
replies
775
views
Code Issue
phyloseq
3.7 years ago klltnq • 0
0
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3
replies
1.1k
views
Installing Packages repeatedly
phyloseq
updated 3.7 years ago by ★ 4.0k • written 3.7 years ago by • 0
0
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1
reply
2.8k
views
Import MetaPhlAn3 to Phyloseq
Metaphlan3 Metagenomics phyloseq
updated 3.7 years ago by ★ 1.1k • written 3.8 years ago by • 0
1
vote
1
reply
4.7k
views
Setting up bioconductor on a Linux server using conda
dada2 conda phyloseq
updated 4.0 years ago by 68k • written 4.0 years ago by • 0
1
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3
replies
1.4k
views
How to assign random effect factor in DESeq2 desing?
StatisticalMethod DESeq2 phyloseq
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
4
votes
3
replies
1.5k
views
Paired-test between two groups within a condition after phyloseq_to_deseq2
DESeq2 phyloseq
updated 4.1 years ago by 43k • written 4.1 years ago by ▴ 10
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0
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1.4k
views
Co-occurrence Network Analysis between Algae and Bacteria
igraph networkanalysis Phylogenetics phyloseq
4.2 years ago Chantel • 0
1
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2
replies
2.9k
views
Bioconductor install error
phyloseq Bioconductor
4.3 years ago Tess • 0
2
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2
replies
2.3k
views
Bioconductor phyloseq taking forever to install?
Bioconductor phyloseq
4.4 years ago garfield320 ▴ 30
0
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1
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1.5k
views
Can I use pseudocounts for differential abundance of OTUs?
metagenomics deseq2 PHYLOSEQ
updated 4.6 years ago by 43k • written 4.7 years ago by • 0
0
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2
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2.4k
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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
4.7 years ago jaiber.solano.i • 0
0
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3
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1.4k
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Nested design- phyloseq_to_deseq
deseq2 Phyloseq Nested
updated 5.0 years ago by 43k • written 5.0 years ago by • 0
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
0
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0
replies
1.1k
views
Problems with creating phyloseq bar plots from a table with species data
phyloseq microbiome analysis
6.1 years ago lm795 ▴ 10
0
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2
replies
1.3k
views
Phyloseq to DESeq2
deseq2 phyloseq
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
0
votes
1
reply
1.9k
views
Import_biom with tree problem
phyloseq mothur 16s
6.4 years ago andrebolerbarros ▴ 20
5
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11
replies
3.2k
views
Error while installing Phyloseq using biocLite
bioclite phyloseq install error
6.5 years ago khp ▴ 30
0
votes
9
replies
2.9k
views
DESEQ2 / Phyloseq contrasts no longer work as before following update
deseq2 phyloseq
6.5 years ago eoin • 0
0
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1
reply
1.1k
views
Invalid class DESeqDataSet object with Phyloseq
deseq2 phyloseq
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 10
0
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1
reply
2.1k
views
Install package phyloseq
installation phyloseq
updated 7.0 years ago by 25k • written 7.0 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 7.1 years ago by ★ 1.2k • written 7.1 years ago by • 0
1
vote
1
reply
1.7k
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
1
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8
replies
6.9k
views
Cannot read Biom file
r biomformat phyloseq
updated 7.4 years ago by ★ 1.1k • written 7.4 years ago by • 0
0
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0
replies
1.6k
views
Problem with ade4 when upgrading to Rstudio 1.1 and OpenR 3.4
phyloseq installation ade4 macos
7.4 years ago sprague • 0
3
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2
replies
4.0k
views
DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
updated 7.5 years ago by 43k • written 7.5 years ago by • 0
0
votes
1
reply
1.6k
views
phyloseq heatmap blank after multiple package updates
phyloseq heatmap
updated 7.5 years ago by ★ 13k • written 7.6 years ago by • 0
1
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3
replies
2.3k
views
Error bars on DESeq2 visuals
deseq2 metagenomics phyloseq ggplot2
7.6 years ago lauren.czaplicki • 0
0
votes
1
reply
1.9k
views
Phyloseq to DESeq2 with multiple variables
deseq2 phyloseq multiple time points
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
0
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0
replies
1.6k
views
Phylogenetic tree from marker genes
ape phyloseq dist metagenomics
7.9 years ago David ▴ 860
1
vote
1
reply
4.1k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
8.0 years ago • updated 7.9 years ago stats134711 • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: DiffBind custom normalization factor by Abbie • 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2? by James W. MacDonald 68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore by Michael Love 43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi by Michael Love 43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
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