Showing : PHYLOSEQ • reset
2
votes
9
replies
22k
views
Error in file(con, “r”) : cannot open the connection
r phyloseq import_biom otu qiime
updated 10.3 years ago by ▴ 20 • written 10.3 years ago by • 0
0
votes
5
replies
8.6k
views
Problems with installation of 'phyloseq
phyloseq
updated 4.5 years ago by ★ 4.0k • written 4.5 years ago by • 0
1
vote
8
replies
7.5k
views
Cannot read Biom file
r biomformat phyloseq
updated 8.3 years ago by ★ 1.1k • written 8.3 years ago by • 0
2
votes
2
replies
7.5k
views
Interpretation of intercept-only model (~1) in DESeq2
deseq2 phyloseq
updated 9.9 years ago by 43k • written 9.9 years ago by ▴ 10
1
vote
1
reply
6.3k
views
Setting up bioconductor on a Linux server using conda
dada2 conda phyloseq
updated 4.9 years ago by 68k • written 4.9 years ago by • 0
0
votes
3
replies
6.0k
views
Phyloseq: How to add sample table to phyloseq object
phyloseq sample_table phyloseq
written 11.1 years ago by ▴ 120
2
votes
1
reply
5.8k
views
does anyone how to create rarefaction curves from a phyloseq object?
phyloseq Phylogenetics
updated 2.9 years ago by ▴ 20 • written 2.9 years ago by • 0
1
vote
1
reply
4.5k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
8.8 years ago stats134711 • 0
3
votes
2
replies
4.4k
views
DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
updated 8.4 years ago by 43k • written 8.4 years ago by • 0
0
votes
6
replies
4.2k
views
Alpha diversity on Rlogtransformed data
deseq2 phyloseq metagenomeseq
10.2 years ago David ▴ 860
0
votes
2
replies
3.8k
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 6.1 years ago by 25k • written 6.1 years ago by • 0
5
votes
11
replies
3.6k
views
Error while installing Phyloseq using biocLite
bioclite phyloseq install error
7.3 years ago khp ▴ 30
1
vote
2
replies
3.4k
views
Bioconductor install error
phyloseq Bioconductor
5.2 years ago Tess • 0
0
votes
9
replies
3.3k
views
DESEQ2 / Phyloseq contrasts no longer work as before following update
deseq2 phyloseq
7.4 years ago eoin • 0
0
votes
1
reply
3.2k
views
Import MetaPhlAn3 to Phyloseq
Metaphlan3 Metagenomics phyloseq
updated 4.6 years ago by ★ 1.1k • written 4.6 years ago by • 0
0
votes
4
replies
3.1k
views
Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings phyloseq
updated 3.9 years ago by 68k • written 3.9 years ago by • 0
2
votes
2
replies
3.0k
views
Bioconductor phyloseq taking forever to install?
Bioconductor phyloseq
5.3 years ago garfield320 ▴ 30
0
votes
3
replies
2.9k
views
I cannot install "microbiome"
GenomeInfoDbData microbiome phyloseq
updated 3.5 years ago by 700 • written 3.5 years ago by • 0
1
vote
10
replies
2.9k
views
Multi-factor Comparison in DESeq 2 Issue
deseq2 phyloseq
updated 11.0 years ago by ★ 7.9k • written 11.0 years ago by • 0
0
votes
2
replies
2.9k
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
5.6 years ago jaiber.solano.i • 0
0
votes
1
reply
2.8k
views
phyloseq merge_samples attempt to set rownames on an object with no dimensions
phyloseq merge_samples rownames error
9.4 years ago newmanss • 0
0
votes
4
replies
2.8k
views
Cannot install Phyloseq and dada2
GenomeInfoDbData phyloseq dada2
4.1 years ago ymtan • 0
0
votes
1
reply
2.8k
views
ggtree facet_plot question using geom_boxplot to plot abundance data corresponding to tree tips
ggtree ggplot2 phyloseq geom_boxplot facet_plot
updated 8.9 years ago by ★ 1.2k • written 8.9 years ago by • 0
0
votes
1
reply
2.8k
views
Error with phyloseq R package with Conda install
software error phyloseq anaconda
written 9.3 years ago by • 0
1
vote
3
replies
2.7k
views
Error bars on DESeq2 visuals
deseq2 metagenomics phyloseq ggplot2
8.5 years ago lauren.czaplicki • 0
3
votes
2
replies
2.6k
views
DESEQ2 (R) design/contrast formula questions
deseq2 phyloseq multiple factor design paired samples
updated 9.9 years ago by ▴ 20 • written 9.9 years ago by ▴ 10
0
votes
1
reply
2.6k
views
phyloseq biom json format conversion needed to hdf5 format for qiime
biom json hdf5 qiime phyloseq
updated 9.3 years ago by ▴ 550 • written 9.3 years ago by • 0
2
votes
1
reply
2.5k
views
Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq microbiome Software
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by ▴ 10
0
votes
1
reply
2.5k
views
Install package phyloseq
installation phyloseq
updated 7.9 years ago by 25k • written 7.9 years ago by • 0
0
votes
3
replies
2.5k
views
Newer version of DESeq2 gives different results
deseq2 phyloseq
updated 9.7 years ago by 43k • written 9.7 years ago by • 0
0
votes
2
replies
2.5k
views
Controlling colours assigned to order in DeSeq2 plot in phyloseq
phyloseq color ggplot2
updated 8.9 years ago by 43k • written 8.9 years ago by • 0
1
vote
2
replies
2.5k
views
DESeqs two-factor two-level, interaction is interested
Sequencing GO phyloseq DESeq2 Sequencing GO phyloseq DESeq2
updated 11.6 years ago by 43k • written 11.6 years ago by ▴ 60
0
votes
1
reply
2.3k
views
tip_glom and annotations?
ggtree treeio phyloseq annotation tip_glom
updated 8.0 years ago by ★ 1.2k • written 8.0 years ago by • 0
2
votes
1
reply
2.3k
views
Using DESeq2 after agglomerating OTUs
phyloseq deseq2 estimatesizefactors
updated 10.2 years ago by 43k • written 10.2 years ago by • 0
0
votes
1
reply
2.2k
views
Import_biom with tree problem
phyloseq mothur 16s
7.3 years ago andrebolerbarros ▴ 20
0
votes
1
reply
2.1k
views
Phyloseq to DESeq2 with multiple variables
deseq2 phyloseq multiple time points
updated 8.6 years ago by 43k • written 8.6 years ago by • 0
0
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0
replies
2.1k
views
How to pool phyloseq data?
phyloseq r
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
0
votes
1
reply
2.1k
views
Co-occurrence Network Analysis between Algae and Bacteria
igraph networkanalysis Phylogenetics phyloseq
updated 11 weeks ago by ▴ 40 • written 5.1 years ago by • 0
1
vote
4
replies
2.1k
views
How can I correctly use phyloseq with Docker?
phylo phyloseq Docker
updated 8 weeks ago by • 0 • written 9 months ago by • 0
2
votes
2
replies
2.0k
views
DESeq2 in phyloseq
deseq2 phyloseq
8.9 years ago sarahmacdonald86 • 0
0
votes
3
replies
2.0k
views
DESeq2 blocking by condition over time
deseq2 phyloseq time course
9.4 years ago akp • 0
0
votes
3
replies
2.0k
views
Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 19 months ago by • 0 • written 2.7 years ago by • 0
0
votes
6
replies
2.0k
views
convert default phylip to sequential phylip
phyloseq Phylogenetics
updated 2.8 years ago by • 0 • written 4.5 years ago by • 0
0
votes
1
reply
1.9k
views
phyloseq heatmap blank after multiple package updates
phyloseq heatmap
updated 8.4 years ago by ★ 13k • written 8.4 years ago by • 0
1
vote
2
replies
1.9k
views
rlogTransformation vs getVarianceStabilizedData
deseq2 r phyloseq
updated 9.2 years ago by 43k • written 9.2 years ago by ▴ 10
1
vote
1
reply
1.9k
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
updated 8.2 years ago by 43k • written 8.2 years ago by • 0
0
votes
0
replies
1.8k
views
Problem with ade4 when upgrading to Rstudio 1.1 and OpenR 3.4
phyloseq installation ade4 macos
8.3 years ago sprague • 0
0
votes
0
replies
1.8k
views
Loading Phyloseq into R- R crashes
software error phyloseq R
11.1 years ago locon833 • 0
0
votes
1
reply
1.8k
views
Can I use pseudocounts for differential abundance of OTUs?
metagenomics deseq2 PHYLOSEQ
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
0
votes
0
replies
1.8k
views
Phylogenetic tree from marker genes
ape phyloseq dist metagenomics
8.8 years ago David ▴ 860
76 results • Page 1 of 2
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Comment: soGGi error by a2sahaaaq2c • 0
Technical discrepancies in software can be frustrating, but finding the right tools for your digital activities is key to a smooth experien…
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the mobile gaming world offers a different kind of strategic challenge. Many users today are shifting from heavy data processing to lighthe…
Comment: Postdoctoral Fellow (Computational Biology / Bioinformatics) - Neuroepigenetics by mudasarnaeem2020 • 0
Promoting UDISE+ Features on Social Media to Increase Awareness https://udisseplus.com/[enter link description here][1] [1]: https://ud…
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To resolve technical errors like installation failures or login issues, first ensure your device allows in the security settings and that…
Comment: soGGi error by shepherl 4.3k
We have tried to contact the soGGi maintainer to have them update the package to the newer version of gglot2 but they have so far been unre…
Votes
Answer: DiffBind differential analysis
Answer: Limma-voom sample weights and impact on DEG numbers
C: Why limma, edgeR, and DESeq did not implement fold change moderation first?
Comment: using limma trend workflow in CAMERA
C: z-score with DESeq2?
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