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 8.5 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
votes
3
replies
1.6k
views
DESeq2 blocking by condition over time
deseq2 phyloseq time course
7.6 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
vote
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
votes
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 8.2 years ago by ▴ 10
0
votes
1
reply
983
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
1.6k
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
837
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
971
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
683
views
Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 13 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
758
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
873
views
Controversial DESEQ2 results
phyloseq DESeq2
updated 22 months ago by 41k • written 23 months ago by • 0
0
votes
3
replies
767
views
Installing Packages repeatedly
phyloseq
updated 2.8 years ago by ★ 3.9k • written 2.8 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
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
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
992
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
853
views
Testing for OTUs with negatively correlated abundances/occurrences
phyloseq
7.8 years ago am39 • 0
0
votes
0
replies
835
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
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Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by camp ▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by ATpoint ★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123 by Gordon Smyth 50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Votes
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
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