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
19k
views
Error in file(con, “r”) : cannot open the connection
r phyloseq import_biom otu qiime
updated 8.5 years ago by ▴ 20 • written 8.5 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
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3
replies
1.6k
views
DESeq2 blocking by condition over time
deseq2 phyloseq time course
7.6 years ago akp • 0
0
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4
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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 9.8 years ago by 41k • written 9.8 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
6.2k
views
Interpretation of intercept-only model (~1) in DESeq2
deseq2 phyloseq
updated 8.1 years ago by 41k • written 8.1 years ago by ▴ 10
0
votes
1
reply
981
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 6.6 years ago by ★ 13k • written 6.6 years ago by • 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
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
1.5k
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
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
834
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
969
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 3.7 years ago by 41k • written 3.7 years ago by • 0
2
votes
2
replies
1.5k
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
680
views
Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 12 days ago by • 0 • written 10 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
755
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
869
views
Controversial DESEQ2 results
phyloseq DESeq2
updated 22 months ago by 41k • written 23 months ago by • 0
0
votes
3
replies
764
views
Installing Packages repeatedly
phyloseq
updated 2.8 years ago by ★ 3.9k • written 2.8 years ago by • 0
0
votes
1
reply
684
views
Purpose of seqtabNoC
phyloseq
updated 2.8 years ago by ★ 3.9k • written 2.8 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
3
replies
997
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
985
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
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
7.1 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 7.1 years ago by ★ 1.2k • written 7.1 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
852
views
Testing for OTUs with negatively correlated abundances/occurrences
phyloseq
7.8 years ago am39 • 0
0
votes
0
replies
834
views
displaying network from microbial count data
phyloseq
7.7 years ago chrisclarkson100 ▴ 50
0
votes
1
reply
4.4k
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
Recent ...
Replies
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
Answer: Log-cpm values from limma
Answer: Log-cpm values from limma
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