Showing : PHYLOSEQ • reset
2
votes
9
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20k
views
Error in file(con, “r”) : cannot open the connection
r phyloseq import_biom otu qiime
updated 9.4 years ago by ▴ 20 • written 9.4 years ago by • 0
0
votes
5
replies
7.7k
views
Problems with installation of 'phyloseq
phyloseq
updated 3.6 years ago by ★ 4.0k • written 3.6 years ago by • 0
2
votes
2
replies
7.0k
views
Interpretation of intercept-only model (~1) in DESeq2
deseq2 phyloseq
updated 9.1 years ago by 43k • written 9.1 years ago by ▴ 10
1
vote
8
replies
6.8k
views
Cannot read Biom file
r biomformat phyloseq
updated 7.4 years ago by ★ 1.1k • written 7.4 years ago by • 0
0
votes
1
reply
5.2k
views
Phyloseq: How to add sample table to phyloseq object
phyloseq sample_table phyloseq
10.2 years ago Brian Smith ▴ 120
1
vote
1
reply
4.7k
views
Setting up bioconductor on a Linux server using conda
dada2 conda phyloseq
updated 4.0 years ago by 68k • written 4.0 years ago by • 0
2
votes
1
reply
4.7k
views
does anyone how to create rarefaction curves from a phyloseq object?
phyloseq Phylogenetics
updated 2.0 years ago by ▴ 20 • written 2.0 years ago by • 0
1
vote
1
reply
4.1k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
7.9 years ago stats134711 • 0
3
votes
2
replies
4.0k
views
DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
updated 7.5 years ago by 43k • written 7.5 years ago by • 0
0
votes
6
replies
3.7k
views
Alpha diversity on Rlogtransformed data
deseq2 phyloseq metagenomeseq
9.3 years ago David ▴ 860
0
votes
2
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3.4k
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 5.3 years ago by 25k • written 5.3 years ago by • 0
5
votes
11
replies
3.2k
views
Error while installing Phyloseq using biocLite
bioclite phyloseq install error
6.5 years ago khp ▴ 30
1
vote
2
replies
2.9k
views
Bioconductor install error
phyloseq Bioconductor
4.3 years ago Tess • 0
0
votes
9
replies
2.9k
views
DESEQ2 / Phyloseq contrasts no longer work as before following update
deseq2 phyloseq
6.5 years ago eoin • 0
0
votes
1
reply
2.8k
views
Import MetaPhlAn3 to Phyloseq
Metaphlan3 Metagenomics phyloseq
updated 3.7 years ago by ★ 1.1k • written 3.7 years ago by • 0
0
votes
4
replies
2.7k
views
Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings phyloseq
updated 3.0 years ago by 68k • written 3.0 years ago by • 0
1
vote
10
replies
2.5k
views
Multi-factor Comparison in DESeq 2 Issue
deseq2 phyloseq
updated 10.1 years ago by ★ 7.9k • written 10.1 years ago by • 0
0
votes
1
reply
2.5k
views
phyloseq merge_samples attempt to set rownames on an object with no dimensions
phyloseq merge_samples rownames error
8.5 years ago newmanss • 0
0
votes
2
replies
2.4k
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
4.7 years ago jaiber.solano.i • 0
0
votes
1
reply
2.4k
views
Error with phyloseq R package with Conda install
software error phyloseq anaconda
written 8.4 years ago by • 0
0
votes
1
reply
2.4k
views
ggtree facet_plot question using geom_boxplot to plot abundance data corresponding to tree tips
ggtree ggplot2 phyloseq geom_boxplot facet_plot
updated 8.0 years ago by ★ 1.2k • written 8.0 years ago by • 0
3
votes
2
replies
2.4k
views
DESEQ2 (R) design/contrast formula questions
deseq2 phyloseq multiple factor design paired samples
updated 9.0 years ago by ▴ 20 • written 9.0 years ago by ▴ 10
0
votes
3
replies
2.4k
views
I cannot install "microbiome"
GenomeInfoDbData microbiome phyloseq
updated 2.6 years ago by 700 • written 2.6 years ago by • 0
1
vote
2
replies
2.3k
views
DESeqs two-factor two-level, interaction is interested
Sequencing GO phyloseq DESeq2 Sequencing GO phyloseq DESeq2
updated 10.7 years ago by 43k • written 10.7 years ago by ▴ 60
0
votes
4
replies
2.3k
views
Cannot install Phyloseq and dada2
GenomeInfoDbData phyloseq dada2
3.2 years ago ymtan • 0
1
vote
3
replies
2.3k
views
Error bars on DESeq2 visuals
deseq2 metagenomics phyloseq ggplot2
7.6 years ago lauren.czaplicki • 0
2
votes
2
replies
2.3k
views
Bioconductor phyloseq taking forever to install?
Bioconductor phyloseq
4.4 years ago garfield320 ▴ 30
0
votes
3
replies
2.3k
views
Newer version of DESeq2 gives different results
deseq2 phyloseq
updated 8.8 years ago by 43k • written 8.8 years ago by • 0
0
votes
1
reply
2.2k
views
phyloseq biom json format conversion needed to hdf5 format for qiime
biom json hdf5 qiime phyloseq
updated 8.4 years ago by ▴ 550 • written 8.4 years ago by • 0
0
votes
2
replies
2.2k
views
Controlling colours assigned to order in DeSeq2 plot in phyloseq
phyloseq color ggplot2
updated 8.1 years ago by 43k • written 8.1 years ago by • 0
2
votes
1
reply
2.1k
views
Using DESeq2 after agglomerating OTUs
phyloseq deseq2 estimatesizefactors
updated 9.3 years ago by 43k • written 9.3 years ago by • 0
0
votes
1
reply
2.1k
views
Install package phyloseq
installation phyloseq
updated 7.0 years ago by 25k • written 7.0 years ago by • 0
0
votes
1
reply
2.0k
views
tip_glom and annotations?
ggtree treeio phyloseq annotation tip_glom
updated 7.1 years ago by ★ 1.2k • written 7.1 years ago by • 0
2
votes
1
reply
1.9k
views
Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq microbiome Software
updated 18 months ago by ★ 4.7k • written 18 months ago by ▴ 10
0
votes
1
reply
1.9k
views
Import_biom with tree problem
phyloseq mothur 16s
6.4 years ago andrebolerbarros ▴ 20
0
votes
1
reply
1.9k
views
Phyloseq to DESeq2 with multiple variables
deseq2 phyloseq multiple time points
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
0
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0
replies
1.8k
views
How to pool phyloseq data?
phyloseq r
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
0
votes
3
replies
1.8k
views
DESeq2 blocking by condition over time
deseq2 phyloseq time course
8.6 years ago akp • 0
2
votes
2
replies
1.7k
views
DESeq2 in phyloseq
deseq2 phyloseq
8.0 years ago sarahmacdonald86 • 0
0
votes
6
replies
1.7k
views
convert default phylip to sequential phylip
phyloseq Phylogenetics
updated 23 months ago by • 0 • written 3.6 years ago by • 0
1
vote
2
replies
1.7k
views
rlogTransformation vs getVarianceStabilizedData
deseq2 r phyloseq
updated 8.3 years ago by 43k • written 8.3 years ago by ▴ 10
0
votes
0
replies
1.7k
views
Loading Phyloseq into R- R crashes
software error phyloseq R
10.2 years ago locon833 • 0
1
vote
1
reply
1.7k
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
0
votes
1
reply
1.6k
views
phyloseq heatmap blank after multiple package updates
phyloseq heatmap
updated 7.5 years ago by ★ 13k • written 7.5 years ago by • 0
0
votes
0
replies
1.6k
views
Problem with ade4 when upgrading to Rstudio 1.1 and OpenR 3.4
phyloseq installation ade4 macos
7.4 years ago sprague • 0
0
votes
0
replies
1.6k
views
Phylogenetic tree from marker genes
ape phyloseq dist metagenomics
7.9 years ago David ▴ 860
0
votes
1
reply
1.5k
views
phyloseq - plot_bar() error
phyloseq plot_bar()
updated 9.4 years ago by ▴ 20 • written 9.4 years ago by ▴ 120
0
votes
1
reply
1.5k
views
DESeqs two-factor two-level, interaction is interested
Sequencing GO phyloseq DESeq2 Sequencing GO phyloseq DESeq2
10.7 years ago Shucong Li ▴ 60
0
votes
1
reply
1.5k
views
Can I use pseudocounts for differential abundance of OTUs?
metagenomics deseq2 PHYLOSEQ
updated 4.6 years ago by 43k • written 4.6 years ago by • 0
4
votes
3
replies
1.4k
views
Paired-test between two groups within a condition after phyloseq_to_deseq2
DESeq2 phyloseq
updated 4.1 years ago by 43k • written 4.1 years ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: DiffBind custom normalization factor by Abbie • 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2? by James W. MacDonald 68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore by Michael Love 43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi by Michael Love 43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
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