Showing : Phyloseq • reset
5
votes
11
replies
2.7k
views
Error while installing Phyloseq using biocLite
bioclite phyloseq install error
5.5 years ago khp ▴ 30
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
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
1
vote
8
replies
5.8k
views
Cannot read Biom file
r biomformat phyloseq
updated 6.5 years ago by ★ 1.0k • written 6.5 years ago by • 0
0
votes
6
replies
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
0
votes
5
replies
6.3k
views
Problems with installation of 'phyloseq
phyloseq
updated 2.7 years ago by ★ 3.9k • written 2.7 years ago by • 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
4
replies
1.8k
views
Cannot install Phyloseq and dada2
GenomeInfoDbData phyloseq dada2
2.3 years ago ymtan • 0
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
3
replies
1.6k
views
I cannot install "microbiome"
GenomeInfoDbData microbiome phyloseq
updated 20 months ago by 690 • written 20 months 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
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
0
votes
3
replies
996
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
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
0
votes
3
replies
762
views
Installing Packages repeatedly
phyloseq
updated 2.8 years ago by ★ 3.9k • written 2.8 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
3
replies
869
views
Controversial DESEQ2 results
phyloseq DESeq2
updated 22 months ago by 41k • written 23 months 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
0
votes
2
replies
1.8k
views
Controlling colours assigned to order in DeSeq2 plot in phyloseq
phyloseq color ggplot2
updated 7.1 years ago by 41k • written 7.1 years ago by • 0
2
votes
2
replies
1.5k
views
DESeq2 in phyloseq
deseq2 phyloseq
7.1 years ago sarahmacdonald86 • 0
0
votes
2
replies
2.9k
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 4.3 years ago by 25k • written 4.3 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
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
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
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
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
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
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
1
reply
2.1k
views
Import MetaPhlAn3 to Phyloseq
Metaphlan3 Metagenomics phyloseq
updated 2.8 years ago by ★ 1.1k • written 2.8 years ago by • 0
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
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
1.3k
views
phyloseq - plot_bar() error
phyloseq plot_bar()
updated 8.4 years ago by ▴ 20 • written 8.5 years ago by ▴ 120
0
votes
1
reply
981
views
Aditional undesired sample
phyloseq
8.1 years ago • updated 8.0 years ago sanrrone • 0
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
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
0
votes
1
reply
2.0k
views
Error with phyloseq R package with Conda install
software error phyloseq anaconda
written 7.5 years ago by • 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
1
vote
1
reply
3.5k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
7.0 years ago stats134711 • 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
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
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
833
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
1
reply
1.5k
views
Import_biom with tree problem
phyloseq mothur 16s
5.5 years ago andrebolerbarros ▴ 20
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
50 results • Page 1 of 1
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Answer: Citation for edgeR user guide by Gordon Smyth 50k
Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You are just making up data? What is the point of this exercise?
Comment: How to retrieve gene ontology GO class? by James W. MacDonald 65k
What do you mean by 'the information'? Do you have things in particular that you want?
Comment: minfi::read.metharray.exp by clacarion • 0
I think its work with `read.metharray.sheet` ```r > sheet <- read.metharray.sheet("/Users/clarachretienneau/Desktop/clock_epigenetic/PJ120…
Comment: minfi::read.metharray.exp by clacarion • 0
Thank you for your response Basti ! I add all the idat files in a unique folder called "idat" and add it in my path ```r > list.files("…
Votes
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
Answer: Cannabis OrgDb
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