Showing : PHYLOSEQ • reset
0
votes
6
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1.4k
views
convert default phylip to sequential phylip
phyloseq Phylogenetics
updated 12 months ago by • 0 • written 2.7 years ago by • 0
0
votes
6
replies
3.2k
views
Alpha diversity on Rlogtransformed data
deseq2 phyloseq metagenomeseq
8.4 years ago David ▴ 860
1
vote
10
replies
2.3k
views
Multi-factor Comparison in DESeq 2 Issue
deseq2 phyloseq
updated 9.2 years ago by ★ 7.9k • written 9.2 years ago by • 0
2
votes
9
replies
20k
views
Error in file(con, “r”) : cannot open the connection
r phyloseq import_biom otu qiime
updated 8.6 years ago by ▴ 20 • written 8.6 years ago by • 0
3
votes
2
replies
2.1k
views
DESEQ2 (R) design/contrast formula questions
deseq2 phyloseq multiple factor design paired samples
updated 8.1 years ago by ▴ 20 • written 8.1 years ago by ▴ 10
0
votes
3
replies
1.6k
views
DESeq2 blocking by condition over time
deseq2 phyloseq time course
7.7 years ago akp • 0
0
votes
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
votes
1
reply
1.9k
views
phyloseq biom json format conversion needed to hdf5 format for qiime
biom json hdf5 qiime phyloseq
updated 7.5 years ago by ▴ 550 • written 7.5 years ago by • 0
1
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2
replies
2.1k
views
DESeqs two-factor two-level, interaction is interested
Sequencing GO phyloseq DESeq2 Sequencing GO phyloseq DESeq2
updated 9.9 years ago by 41k • written 9.9 years ago by ▴ 60
0
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1
reply
1.3k
views
DESeqs two-factor two-level, interaction is interested
Sequencing GO phyloseq DESeq2 Sequencing GO phyloseq DESeq2
9.8 years ago Shucong Li ▴ 60
0
votes
1
reply
1.3k
views
phyloseq - plot_bar() error
phyloseq plot_bar()
updated 8.5 years ago by ▴ 20 • written 8.5 years ago by ▴ 120
2
votes
2
replies
6.3k
views
Interpretation of intercept-only model (~1) in DESeq2
deseq2 phyloseq
updated 8.2 years ago by 41k • written 8.2 years ago by ▴ 10
0
votes
1
reply
986
views
Aditional undesired sample
phyloseq
8.1 years ago sanrrone • 0
0
votes
3
replies
2.0k
views
Newer version of DESeq2 gives different results
deseq2 phyloseq
updated 7.9 years ago by 41k • written 7.9 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
votes
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
3
votes
2
replies
3.3k
views
DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
updated 6.7 years ago by 41k • written 6.7 years ago by • 0
1
vote
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
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
0
votes
1
reply
1.6k
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
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
votes
1
reply
840
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
9
replies
2.4k
views
DESEQ2 / Phyloseq contrasts no longer work as before following update
deseq2 phyloseq
5.6 years ago eoin • 0
0
votes
2
replies
976
views
Phyloseq to DESeq2
deseq2 phyloseq
updated 5.3 years ago by 41k • written 5.3 years ago by • 0
0
votes
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
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
votes
1
reply
1.1k
views
Can I use pseudocounts for differential abundance of OTUs?
metagenomics deseq2 PHYLOSEQ
updated 3.8 years ago by 41k • written 3.8 years ago by • 0
2
votes
2
replies
1.6k
views
Bioconductor phyloseq taking forever to install?
Bioconductor phyloseq
3.5 years ago garfield320 ▴ 30
1
vote
2
replies
2.3k
views
Bioconductor install error
phyloseq Bioconductor
3.4 years ago Tess • 0
0
votes
1
reply
705
views
Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 21 days ago by • 0 • written 11 months 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
1
vote
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
1
vote
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
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
764
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
votes
3
replies
886
views
Controversial DESEQ2 results
phyloseq DESeq2
updated 23 months ago by 41k • written 23 months ago by • 0
0
votes
3
replies
775
views
Installing Packages repeatedly
phyloseq
updated 2.9 years ago by ★ 3.9k • written 2.9 years ago by • 0
0
votes
1
reply
688
views
Purpose of seqtabNoC
phyloseq
updated 2.9 years ago by ★ 3.9k • written 2.9 years ago by • 0
0
votes
5
replies
6.4k
views
Problems with installation of 'phyloseq
phyloseq
updated 2.8 years ago by ★ 3.9k • written 2.8 years ago by • 0
0
votes
3
replies
1.0k
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
2
votes
1
reply
1.0k
views
Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq microbiome Software
updated 7 months ago by ★ 4.1k • written 7 months ago by ▴ 10
2
votes
1
reply
1.9k
views
Using DESeq2 after agglomerating OTUs
phyloseq deseq2 estimatesizefactors
updated 8.4 years ago by 41k • written 8.4 years ago by • 0
1
vote
2
replies
1.4k
views
rlogTransformation vs getVarianceStabilizedData
deseq2 r phyloseq
updated 7.4 years ago by 41k • written 7.4 years ago by ▴ 10
2
votes
2
replies
1.5k
views
DESeq2 in phyloseq
deseq2 phyloseq
7.2 years ago sarahmacdonald86 • 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 7.2 years ago by ★ 1.2k • written 7.2 years ago by • 0
0
votes
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
votes
0
replies
858
views
Testing for OTUs with negatively correlated abundances/occurrences
phyloseq
7.8 years ago am39 • 0
0
votes
0
replies
836
views
displaying network from microbial count data
phyloseq
7.8 years ago chrisclarkson100 ▴ 50
0
votes
1
reply
4.5k
views
Phyloseq: How to add sample table to phyloseq object
phyloseq sample_table phyloseq
9.3 years ago Brian Smith ▴ 120
0
votes
1
reply
2.2k
views
phyloseq merge_samples attempt to set rownames on an object with no dimensions
phyloseq merge_samples rownames error
7.6 years ago newmanss • 0
50 results • Page 1 of 1
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Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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