Showing : Phyloseq • reset
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2
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752
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Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 3 days ago by • 0 • written 11 months ago by • 0
2
votes
1
reply
1.1k
views
Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq microbiome Software
updated 8 months ago by ★ 4.1k • written 8 months ago by ▴ 10
0
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0
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384
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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
9 months ago Mohamed ▴ 30
0
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6
replies
1.4k
views
convert default phylip to sequential phylip
phyloseq Phylogenetics
updated 12 months ago by • 0 • written 2.7 years ago by • 0
1
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1
reply
2.6k
views
does anyone how to create rarefaction curves from a phyloseq object?
phyloseq Phylogenetics
updated 14 months ago by ▴ 10 • written 14 months ago by • 0
0
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3
replies
1.7k
views
I cannot install "microbiome"
GenomeInfoDbData microbiome phyloseq
updated 21 months ago by 700 • written 21 months ago by • 0
0
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1
reply
682
views
error installing phyloseq
phyloseq
updated 23 months ago by 3.9k • written 23 months ago by • 0
0
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3
replies
910
views
Controversial DESEQ2 results
phyloseq DESeq2
updated 23 months ago by 42k • written 23 months ago by • 0
0
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0
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508
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Association between ohylum and genus on microbiome data sets.
phyloseq
2.0 years ago Edmond • 0
0
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0
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1.4k
views
How to pool phyloseq data?
phyloseq r
updated 2.2 years ago by 42k • written 2.2 years ago by • 0
0
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4
replies
1.9k
views
Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings phyloseq
updated 2.2 years ago by 65k • written 2.2 years ago by • 0
0
votes
1
reply
778
views
Deseq workflow for phyloseq object and complicated data structure?
phyloseq DESeq2
updated 2.3 years ago by 42k • written 2.3 years ago by • 0
0
votes
4
replies
1.8k
views
Cannot install Phyloseq and dada2
GenomeInfoDbData phyloseq dada2
2.3 years ago ymtan • 0
0
votes
1
reply
704
views
Error in 'differential_abundance'
phyloseq devtools
updated 2.4 years ago by 42k • written 2.4 years ago by • 0
0
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0
replies
783
views
Construct a phyloseq object directly from the dada2 outputs
phyloseq dada2
2.7 years ago Manijeh • 0
0
votes
3
replies
1.0k
views
DESeq2: difficulty with contrasts and main effects
DESeq2 phyloseq contrasts
updated 2.8 years ago by ★ 3.9k • written 2.8 years ago by • 0
0
votes
5
replies
6.5k
views
Problems with installation of 'phyloseq
phyloseq
updated 2.8 years ago by ★ 3.9k • written 2.8 years ago by • 0
0
votes
1
reply
701
views
Purpose of seqtabNoC
phyloseq
updated 2.9 years ago by ★ 3.9k • written 2.9 years ago by • 0
0
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0
replies
743
views
Construct Phylogenetic Tree
phyloseq
2.9 years ago klltnq • 0
0
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0
replies
627
views
Code Issue
phyloseq
2.9 years ago klltnq • 0
0
votes
3
replies
799
views
Installing Packages repeatedly
phyloseq
updated 2.9 years ago by ★ 3.9k • written 2.9 years ago by • 0
0
votes
1
reply
2.2k
views
Import MetaPhlAn3 to Phyloseq
Metaphlan3 Metagenomics phyloseq
updated 2.9 years ago by ★ 1.1k • written 2.9 years ago by • 0
1
vote
1
reply
3.7k
views
Setting up bioconductor on a Linux server using conda
dada2 conda phyloseq
updated 3.1 years ago by 65k • written 3.2 years ago by • 0
1
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3
replies
1.1k
views
How to assign random effect factor in DESeq2 desing?
StatisticalMethod DESeq2 phyloseq
updated 3.2 years ago by 42k • written 3.2 years ago by • 0
4
votes
3
replies
1.2k
views
Paired-test between two groups within a condition after phyloseq_to_deseq2
DESeq2 phyloseq
updated 3.3 years ago by 42k • written 3.3 years ago by ▴ 10
0
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0
replies
1.1k
views
Co-occurrence Network Analysis between Algae and Bacteria
igraph networkanalysis Phylogenetics phyloseq
3.4 years ago Chantel • 0
1
vote
2
replies
2.4k
views
Bioconductor install error
phyloseq Bioconductor
3.5 years ago Tess • 0
2
votes
2
replies
1.6k
views
Bioconductor phyloseq taking forever to install?
Bioconductor phyloseq
3.6 years ago garfield320 ▴ 30
0
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1
reply
1.1k
views
Can I use pseudocounts for differential abundance of OTUs?
metagenomics deseq2 PHYLOSEQ
updated 3.8 years ago by 42k • written 3.8 years ago by • 0
0
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2
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1.9k
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
3.9 years ago jaiber.solano.i • 0
0
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3
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1.0k
views
Nested design- phyloseq_to_deseq
deseq2 Phyloseq Nested
updated 4.1 years ago by 42k • written 4.1 years ago by • 0
0
votes
2
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2.9k
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 4.4 years ago by 25k • written 4.4 years ago by • 0
0
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0
replies
835
views
Problems with creating phyloseq bar plots from a table with species data
phyloseq microbiome analysis
5.3 years ago lm795 ▴ 10
0
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2
replies
988
views
Phyloseq to DESeq2
deseq2 phyloseq
updated 5.3 years ago by 42k • written 5.3 years ago by • 0
0
votes
1
reply
1.6k
views
Import_biom with tree problem
phyloseq mothur 16s
5.6 years ago andrebolerbarros ▴ 20
5
votes
11
replies
2.8k
views
Error while installing Phyloseq using biocLite
bioclite phyloseq install error
5.6 years ago khp ▴ 30
0
votes
9
replies
2.4k
views
DESEQ2 / Phyloseq contrasts no longer work as before following update
deseq2 phyloseq
5.7 years ago eoin • 0
0
votes
1
reply
852
views
Invalid class DESeqDataSet object with Phyloseq
deseq2 phyloseq
updated 5.8 years ago by 42k • written 5.8 years ago by ▴ 10
0
votes
1
reply
1.7k
views
Install package phyloseq
installation phyloseq
updated 6.2 years ago by 25k • written 6.2 years ago by • 0
0
votes
1
reply
1.6k
views
tip_glom and annotations?
ggtree treeio phyloseq annotation tip_glom
updated 6.3 years ago by ★ 1.2k • written 6.3 years ago by • 0
1
vote
1
reply
1.4k
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
updated 6.5 years ago by 42k • written 6.5 years ago by • 0
1
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8
replies
5.9k
views
Cannot read Biom file
r biomformat phyloseq
updated 6.5 years ago by ★ 1.0k • written 6.5 years ago by • 0
0
votes
0
replies
1.3k
views
Problem with ade4 when upgrading to Rstudio 1.1 and OpenR 3.4
phyloseq installation ade4 macos
6.6 years ago sprague • 0
3
votes
2
replies
3.4k
views
DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
updated 6.7 years ago by 42k • written 6.7 years ago by • 0
0
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1
reply
1.3k
views
phyloseq heatmap blank after multiple package updates
phyloseq heatmap
updated 6.7 years ago by ★ 13k • written 6.7 years ago by • 0
1
vote
3
replies
1.9k
views
Error bars on DESeq2 visuals
deseq2 metagenomics phyloseq ggplot2
6.8 years ago lauren.czaplicki • 0
0
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1
reply
1.5k
views
Phyloseq to DESeq2 with multiple variables
deseq2 phyloseq multiple time points
updated 6.8 years ago by 42k • written 6.8 years ago by • 0
0
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0
replies
1.3k
views
Phylogenetic tree from marker genes
ape phyloseq dist metagenomics
7.1 years ago David ▴ 860
1
vote
1
reply
3.5k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
7.1 years ago stats134711 • 0
0
votes
1
reply
2.1k
views
ggtree facet_plot question using geom_boxplot to plot abundance data corresponding to tree tips
ggtree ggplot2 phyloseq geom_boxplot facet_plot
updated 7.2 years ago by ★ 1.2k • written 7.2 years ago by • 0
50 results • Page 1 of 1
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Answer: all variables in design formula must be columns in colData (Deseq2) error by ATpoint ★ 4.1k
Your code is poorly readable. Suggest you select and then highlight with markdown using the `10101` button. Generally, colData(dds) must…
Answer: Subsetting RNAseq data | voomaByGroup() by Gordon Smyth 50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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