Showing : Phyloseq • reset
0
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681
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Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 12 days ago by • 0 • written 10 months ago by • 0
2
votes
1
reply
986
views
Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq microbiome Software
updated 7 months ago by ★ 4.0k • written 7 months ago by ▴ 10
0
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0
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356
views
Try to understand better how to set out an effective sample size within the MetagenomSeq package in microbiome ?
Metagenomics metagenomeSeq microbiome phyloseq microbiomeDataSets
8 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
2.4k
views
does anyone how to create rarefaction curves from a phyloseq object?
phyloseq Phylogenetics
updated 13 months ago by ▴ 10 • written 13 months ago by • 0
0
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3
replies
1.6k
views
I cannot install "microbiome"
GenomeInfoDbData microbiome phyloseq
updated 20 months ago by 690 • written 20 months ago by • 0
0
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1
reply
658
views
error installing phyloseq
phyloseq
updated 22 months ago by 3.8k • written 22 months ago by • 0
0
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3
replies
870
views
Controversial DESEQ2 results
phyloseq DESeq2
updated 22 months ago by 41k • written 23 months ago by • 0
0
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0
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494
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Association between ohylum and genus on microbiome data sets.
phyloseq
24 months ago Edmond • 0
0
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0
replies
1.3k
views
How to pool phyloseq data?
phyloseq r
updated 2.1 years ago by 41k • written 2.1 years ago by • 0
0
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4
replies
1.8k
views
Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings phyloseq
updated 2.1 years ago by 65k • written 2.1 years ago by • 0
0
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1
reply
757
views
Deseq workflow for phyloseq object and complicated data structure?
phyloseq DESeq2
updated 2.3 years ago by 41k • written 2.3 years ago by • 0
0
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4
replies
1.8k
views
Cannot install Phyloseq and dada2
GenomeInfoDbData phyloseq dada2
2.3 years ago ymtan • 0
0
votes
1
reply
684
views
Error in 'differential_abundance'
phyloseq devtools
updated 2.3 years ago by 41k • written 2.3 years ago by • 0
0
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0
replies
761
views
Construct a phyloseq object directly from the dada2 outputs
phyloseq dada2
2.7 years ago Manijeh • 0
0
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3
replies
1000
views
DESeq2: difficulty with contrasts and main effects
DESeq2 phyloseq contrasts
updated 2.7 years ago by ★ 3.9k • written 2.7 years ago by • 0
0
votes
5
replies
6.4k
views
Problems with installation of 'phyloseq
phyloseq
updated 2.7 years ago by ★ 3.9k • written 2.7 years ago by • 0
0
votes
1
reply
685
views
Purpose of seqtabNoC
phyloseq
updated 2.8 years ago by ★ 3.9k • written 2.8 years ago by • 0
0
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0
replies
726
views
Construct Phylogenetic Tree
phyloseq
2.8 years ago klltnq • 0
0
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0
replies
619
views
Code Issue
phyloseq
2.8 years ago klltnq • 0
0
votes
3
replies
765
views
Installing Packages repeatedly
phyloseq
updated 2.8 years ago by ★ 3.9k • written 2.8 years ago by • 0
0
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1
reply
2.1k
views
Import MetaPhlAn3 to Phyloseq
Metaphlan3 Metagenomics phyloseq
updated 2.8 years ago by ★ 1.1k • written 2.8 years ago by • 0
1
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1
reply
3.6k
views
Setting up bioconductor on a Linux server using conda
dada2 conda phyloseq
updated 3.1 years ago by 65k • written 3.1 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 41k • written 3.2 years ago by • 0
4
votes
3
replies
1.1k
views
Paired-test between two groups within a condition after phyloseq_to_deseq2
DESeq2 phyloseq
updated 3.2 years ago by 41k • written 3.2 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
3.3 years ago Chantel • 0
1
vote
2
replies
2.3k
views
Bioconductor install error
phyloseq Bioconductor
3.4 years ago Tess • 0
2
votes
2
replies
1.5k
views
Bioconductor phyloseq taking forever to install?
Bioconductor phyloseq
3.5 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 3.7 years ago by 41k • written 3.7 years ago by • 0
0
votes
2
replies
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
3.8 years ago jaiber.solano.i • 0
0
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3
replies
1.0k
views
Nested design- phyloseq_to_deseq
deseq2 Phyloseq Nested
updated 4.1 years ago by 41k • written 4.1 years ago by • 0
0
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2
replies
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
820
views
Problems with creating phyloseq bar plots from a table with species data
phyloseq microbiome analysis
5.2 years ago lm795 ▴ 10
0
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2
replies
970
views
Phyloseq to DESeq2
deseq2 phyloseq
updated 5.3 years ago by 41k • written 5.3 years ago by • 0
0
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1
reply
1.5k
views
Import_biom with tree problem
phyloseq mothur 16s
5.5 years ago andrebolerbarros ▴ 20
5
votes
11
replies
2.8k
views
Error while installing Phyloseq using biocLite
bioclite phyloseq install error
5.5 years ago khp ▴ 30
0
votes
9
replies
2.4k
views
DESEQ2 / Phyloseq contrasts no longer work as before following update
deseq2 phyloseq
5.6 years ago eoin • 0
0
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1
reply
836
views
Invalid class DESeqDataSet object with Phyloseq
deseq2 phyloseq
updated 5.7 years ago by 41k • written 5.7 years ago by ▴ 10
0
votes
1
reply
1.7k
views
Install package phyloseq
installation phyloseq
updated 6.1 years ago by 25k • written 6.1 years ago by • 0
0
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1
reply
1.5k
views
tip_glom and annotations?
ggtree treeio phyloseq annotation tip_glom
updated 6.2 years ago by ★ 1.2k • written 6.2 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 6.4 years ago by 41k • written 6.4 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
1.2k
views
Problem with ade4 when upgrading to Rstudio 1.1 and OpenR 3.4
phyloseq installation ade4 macos
6.5 years ago sprague • 0
3
votes
2
replies
3.3k
views
DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
updated 6.6 years ago by 41k • written 6.6 years ago by • 0
0
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1
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1.3k
views
phyloseq heatmap blank after multiple package updates
phyloseq heatmap
updated 6.6 years ago by ★ 13k • written 6.6 years ago by • 0
1
vote
3
replies
1.9k
views
Error bars on DESeq2 visuals
deseq2 metagenomics phyloseq ggplot2
6.7 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 41k • 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
7.0 years ago David ▴ 860
1
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1
reply
3.5k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
7.0 years ago stats134711 • 0
0
votes
1
reply
2.0k
views
ggtree facet_plot question using geom_boxplot to plot abundance data corresponding to tree tips
ggtree ggplot2 phyloseq geom_boxplot facet_plot
updated 7.1 years ago by ★ 1.2k • written 7.1 years ago by • 0
50 results • Page 1 of 1
Recent ...
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Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…
Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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