Showing : phyloseq • reset
1
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122
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Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq microbiome Software
updated 7 days ago by ★ 3.4k • written 8 days ago by • 0
0
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0
replies
97
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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
5 weeks ago Mohamed ▴ 20
0
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1
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237
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Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
written 3 months ago by • 0
0
votes
6
replies
1.1k
views
convert default phylip to sequential phylip
phyloseq Phylogenetics
updated 5 months ago by • 0 • written 2.1 years ago by • 0
1
vote
1
reply
1.0k
views
does anyone how to create rarefaction curves from a phyloseq object?
phyloseq Phylogenetics
updated 6 months ago by ▴ 10 • written 6 months ago by • 0
0
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3
replies
1.0k
views
I cannot install "microbiome"
GenomeInfoDbData microbiome phyloseq
updated 13 months ago by 680 • written 13 months ago by • 0
0
votes
1
reply
440
views
error installing phyloseq
phyloseq
updated 15 months ago by 3.5k • written 15 months ago by • 0
0
votes
3
replies
630
views
Controversial DESEQ2 results
phyloseq DESeq2
updated 15 months ago by 40k • written 15 months ago by • 0
0
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0
replies
331
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Association between ohylum and genus on microbiome data sets.
phyloseq
16 months ago Edmond • 0
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0
replies
1.0k
views
How to pool phyloseq data?
phyloseq r
updated 18 months ago by 40k • written 18 months ago by • 0
0
votes
4
replies
1.3k
views
Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings phyloseq
updated 18 months ago by 63k • written 18 months ago by • 0
0
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1
reply
559
views
Deseq workflow for phyloseq object and complicated data structure?
phyloseq DESeq2
updated 20 months ago by 40k • written 20 months ago by • 0
0
votes
4
replies
1.4k
views
Cannot install Phyloseq and dada2
GenomeInfoDbData phyloseq dada2
20 months ago ymtan • 0
0
votes
1
reply
474
views
Error in 'differential_abundance'
phyloseq devtools
updated 20 months ago by 40k • written 20 months ago by • 0
0
votes
0
replies
581
views
Construct a phyloseq object directly from the dada2 outputs
phyloseq dada2
2.1 years ago Manijeh • 0
0
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3
replies
734
views
DESeq2: difficulty with contrasts and main effects
DESeq2 phyloseq contrasts
updated 2.1 years ago by 3.8k • written 2.1 years ago by • 0
0
votes
5
replies
4.9k
views
Problems with installation of 'phyloseq
phyloseq
updated 2.1 years ago by 3.8k • written 2.2 years ago by • 0
0
votes
1
reply
521
views
Purpose of seqtabNoC
phyloseq
updated 2.2 years ago by 3.8k • written 2.2 years ago by • 0
0
votes
0
replies
551
views
Construct Phylogenetic Tree
phyloseq
2.2 years ago klltnq • 0
0
votes
0
replies
483
views
Code Issue
phyloseq
2.2 years ago klltnq • 0
0
votes
3
replies
594
views
Installing Packages repeatedly
phyloseq
updated 2.2 years ago by 3.8k • written 2.2 years ago by • 0
0
votes
1
reply
1.7k
views
Import MetaPhlAn3 to Phyloseq
Metaphlan3 Metagenomics phyloseq
updated 2.3 years ago by 1.1k • written 2.3 years ago by • 0
1
vote
1
reply
2.8k
views
Setting up bioconductor on a Linux server using conda
dada2 conda phyloseq
updated 2.5 years ago by 63k • written 2.5 years ago by • 0
1
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3
replies
813
views
How to assign random effect factor in DESeq2 desing?
StatisticalMethod DESeq2 phyloseq
updated 2.6 years ago by 40k • written 2.6 years ago by • 0
4
votes
3
replies
875
views
Paired-test between two groups within a condition after phyloseq_to_deseq2
DESeq2 phyloseq
updated 2.6 years ago by 40k • written 2.6 years ago by ▴ 10
0
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0
replies
845
views
Co-occurrence Network Analysis between Algae and Bacteria
igraph networkanalysis Phylogenetics phyloseq
2.7 years ago Chantel • 0
1
vote
2
replies
1.9k
views
Bioconductor install error
phyloseq Bioconductor
2.8 years ago Tess • 0
2
votes
2
replies
1.2k
views
Bioconductor phyloseq taking forever to install?
Bioconductor phyloseq
2.9 years ago garfield320 ▴ 30
0
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1
reply
903
views
Can I use pseudocounts for differential abundance of OTUs?
metagenomics deseq2 PHYLOSEQ
updated 3.2 years ago by 40k • written 3.2 years ago by • 0
0
votes
2
replies
1.5k
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
3.2 years ago jaiber.solano.i • 0
0
votes
3
replies
793
views
Nested design- phyloseq_to_deseq
deseq2 Phyloseq Nested
updated 3.5 years ago by 40k • written 3.5 years ago by • 0
0
votes
2
replies
2.5k
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 3.8 years ago by 25k • written 3.8 years ago by • 0
0
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0
replies
655
views
Problems with creating phyloseq bar plots from a table with species data
phyloseq microbiome analysis
4.6 years ago lm795 ▴ 10
0
votes
2
replies
810
views
Phyloseq to DESeq2
deseq2 phyloseq
updated 4.7 years ago by 40k • written 4.7 years ago by • 0
0
votes
1
reply
1.3k
views
Import_biom with tree problem
phyloseq mothur 16s
4.9 years ago andrebolerbarros ▴ 20
5
votes
11
replies
2.3k
views
Error while installing Phyloseq using biocLite
bioclite phyloseq install error
5.0 years ago khp ▴ 30
0
votes
9
replies
2.0k
views
DESEQ2 / Phyloseq contrasts no longer work as before following update
deseq2 phyloseq
5.0 years ago eoin • 0
0
votes
1
reply
647
views
Invalid class DESeqDataSet object with Phyloseq
deseq2 phyloseq
updated 5.1 years ago by 40k • written 5.1 years ago by ▴ 10
0
votes
1
reply
1.4k
views
Install package phyloseq
installation phyloseq
updated 5.5 years ago by 25k • written 5.5 years ago by • 0
0
votes
1
reply
1.2k
views
tip_glom and annotations?
ggtree treeio phyloseq annotation tip_glom
updated 5.6 years ago by ★ 1.2k • written 5.6 years ago by • 0
1
vote
1
reply
1.2k
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
updated 5.8 years ago by 40k • written 5.8 years ago by • 0
1
vote
8
replies
4.9k
views
Cannot read Biom file
r biomformat phyloseq
updated 5.9 years ago by ▴ 990 • written 5.9 years ago by • 0
0
votes
0
replies
1.0k
views
Problem with ade4 when upgrading to Rstudio 1.1 and OpenR 3.4
phyloseq installation ade4 macos
5.9 years ago sprague • 0
3
votes
2
replies
2.8k
views
DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
updated 6.0 years ago by 40k • written 6.0 years ago by • 0
0
votes
1
reply
1.1k
views
phyloseq heatmap blank after multiple package updates
phyloseq heatmap
updated 6.0 years ago by 13k • written 6.1 years ago by • 0
1
vote
3
replies
1.6k
views
Error bars on DESeq2 visuals
deseq2 metagenomics phyloseq ggplot2
6.1 years ago lauren.czaplicki • 0
0
votes
1
reply
1.3k
views
Phyloseq to DESeq2 with multiple variables
deseq2 phyloseq multiple time points
updated 6.2 years ago by 40k • written 6.2 years ago by • 0
0
votes
0
replies
1.1k
views
Phylogenetic tree from marker genes
ape phyloseq dist metagenomics
6.4 years ago David ▴ 860
1
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1
reply
3.1k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
6.5 years ago stats134711 • 0
0
votes
1
reply
1.8k
views
ggtree facet_plot question using geom_boxplot to plot abundance data corresponding to tree tips
ggtree ggplot2 phyloseq geom_boxplot facet_plot
updated 6.6 years ago by ★ 1.2k • written 6.6 years ago by • 0
50 results • Page 1 of 1
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Comment: DataFrame Construction With Non-standard Column by ATpoint ★ 3.4k
Out of interest, `SimpleList()` works without `I()`, why is that?
Answer: DataFrame Construction With Non-standard Column by Hervé Pagès 16k
You need to protect the list by wrapping it in `I()`, otherwise the `DataFrame()` constructor interprets it as a list of 3 columns (so it t…
Comment: Speeding up of DelayedArray::write_block() by Koki ▴ 10
Thank you, I have a very clear understanding of the situation. > COO_Sparse_HDF5RealizationSink(), writeHDF5SparseArray(), COO_H5SparseArr…
Comment: Speeding up of DelayedArray::write_block() by Koki ▴ 10
There are a few places inside my `DelayedTensor` package that use `SparseArraySeed`. Will these stop working in next coming BioC 3.18, whe…
Comment: DelayedArray::read_sparse_block by Hervé Pagès 16k
No. But I will need to modify the `write_block()` method for TENxRealizationSink implemented in **HDF5Array** to make it handle blocks that…
Votes
Answer: Further analysis after limma regression output
A: collapseReplicates in DESeq2
Answer: DataFrame Construction With Non-standard Column
Steps needed to change design (relevel factors) in DESeq2
Steps needed to change design (relevel factors) in DESeq2
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