Showing : phyloseq • reset
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57
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convert default phylip to sequential phylip
phyloseq Phylogenetics
written 22 days ago by • 0
0
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0
replies
68
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Construct a phyloseq object directly from the dada2 outputs
phyloseq dada2
4 weeks ago Manijeh • 0
0
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3
replies
114
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DESeq2: difficulty with contrasts and main effects
DESeq2 phyloseq contrasts
updated 6 weeks ago by 3.4k • written 6 weeks ago by • 0
0
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5
replies
455
views
Problems with installation of 'phyloseq
phyloseq
updated 6 weeks ago by 3.4k • written 6 weeks ago by • 0
0
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1
reply
103
views
Purpose of seqtabNoC
phyloseq
updated 12 weeks ago by 3.4k • written 12 weeks ago by • 0
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0
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83
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Construct Phylogenetic Tree
phyloseq
12 weeks ago klltnq • 0
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0
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93
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Code Issue
phyloseq
12 weeks ago klltnq • 0
0
votes
3
replies
145
views
Installing Packages repeatedly
phyloseq
updated 12 weeks ago by 3.4k • written 12 weeks ago by • 0
0
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1
reply
191
views
Import MetaPhlAn3 to Phyloseq
Metaphlan3 Metagenomics phyloseq
updated 12 weeks ago by 1.1k • written 12 weeks ago by • 0
0
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1
reply
327
views
Setting up bioconductor on a Linux server using conda
dada2 conda phyloseq
updated 5 months ago by 58k • written 5 months ago by • 0
1
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3
replies
225
views
How to assign random effect factor in DESeq2 desing?
StatisticalMethod DESeq2 phyloseq
updated 7 months ago by 34k • written 7 months ago by • 0
4
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3
replies
256
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Paired-test between two groups within a condition after phyloseq_to_deseq2
DESeq2 phyloseq
updated 7 months ago by 34k • written 7 months ago by ▴ 10
0
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0
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235
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Co-occurrence Network Analysis between Algae and Bacteria
igraph networkanalysis Phylogenetics phyloseq
8 months ago Chantel • 0
1
vote
2
replies
566
views
Bioconductor install error
phyloseq Bioconductor
9 months ago Tess • 0
2
votes
2
replies
338
views
Bioconductor phyloseq taking forever to install?
Bioconductor phyloseq
10 months ago garfield320 ▴ 30
0
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1
reply
250
views
Can I use pseudocounts for differential abundance of OTUs?
metagenomics deseq2 PHYLOSEQ
updated 13 months ago by 34k • written 13 months ago by • 0
0
votes
2
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240
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
14 months ago jaiber.solano.i • 0
0
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3
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194
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Nested design- phyloseq_to_deseq
deseq2 Phyloseq Nested
updated 17 months ago by 34k • written 17 months ago by • 0
0
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2
replies
1.0k
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 21 months ago by 25k • written 21 months ago by • 0
0
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0
replies
272
views
Problems with creating phyloseq bar plots from a table with species data
phyloseq microbiome analysis
2.6 years ago lm795 ▴ 10
0
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2
replies
422
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Phyloseq to DESeq2
deseq2 phyloseq
updated 2.7 years ago by 34k • written 2.7 years ago by • 0
0
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1
reply
581
views
Import_biom with tree problem
phyloseq mothur 16s
2.9 years ago andrebolerbarros ▴ 10
5
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11
replies
1.6k
views
Error while installing Phyloseq using biocLite
bioclite phyloseq install error
2.9 years ago khp ▴ 30
0
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9
replies
1.0k
views
DESEQ2 / Phyloseq contrasts no longer work as before following update
deseq2 phyloseq
3.0 years ago eoin • 0
0
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1
reply
381
views
Invalid class DESeqDataSet object with Phyloseq
deseq2 phyloseq
updated 3.1 years ago by 34k • written 3.1 years ago by ▴ 10
0
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1
reply
705
views
Install package phyloseq
installation phyloseq
updated 3.5 years ago by 25k • written 3.5 years ago by • 0
0
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1
reply
667
views
tip_glom and annotations?
ggtree treeio phyloseq annotation tip_glom
updated 3.6 years ago by ★ 1.2k • written 3.6 years ago by • 0
1
vote
1
reply
690
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
updated 3.8 years ago by 34k • written 3.8 years ago by • 0
1
vote
8
replies
2.8k
views
Cannot read Biom file
r biomformat phyloseq
updated 3.9 years ago by ▴ 980 • written 3.9 years ago by • 0
0
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0
replies
545
views
Problem with ade4 when upgrading to Rstudio 1.1 and OpenR 3.4
phyloseq installation ade4 macos
3.9 years ago sprague • 0
2
votes
2
replies
1.6k
views
DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
updated 4.0 years ago by 34k • written 4.0 years ago by • 0
0
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1
reply
668
views
phyloseq heatmap blank after multiple package updates
phyloseq heatmap
updated 4.0 years ago by 13k • written 4.0 years ago by • 0
1
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3
replies
963
views
Error bars on DESeq2 visuals
deseq2 metagenomics phyloseq ggplot2
4.1 years ago lauren.czaplicki • 0
0
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1
reply
785
views
Phyloseq to DESeq2 with multiple variables
deseq2 phyloseq multiple time points
updated 4.2 years ago by 34k • written 4.2 years ago by • 0
0
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0
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652
views
Phylogenetic tree from marker genes
ape phyloseq dist metagenomics
4.4 years ago David ▴ 860
1
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1
reply
1.9k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
4.4 years ago stats134711 • 0
0
votes
1
reply
1.2k
views
ggtree facet_plot question using geom_boxplot to plot abundance data corresponding to tree tips
ggtree ggplot2 phyloseq geom_boxplot facet_plot
updated 4.5 years ago by ★ 1.2k • written 4.5 years ago by • 0
2
votes
2
replies
851
views
DESeq2 in phyloseq
deseq2 phyloseq
4.5 years ago sarahmacdonald86 • 0
0
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2
replies
1.1k
views
Controlling colours assigned to order in DeSeq2 plot in phyloseq
phyloseq color ggplot2
updated 4.5 years ago by 34k • written 4.5 years ago by • 0
1
vote
2
replies
836
views
rlogTransformation vs getVarianceStabilizedData
deseq2 r phyloseq
updated 4.8 years ago by 34k • written 4.8 years ago by ▴ 10
0
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0
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1.1k
views
Error with phyloseq R package with Conda install
software error phyloseq anaconda
4.9 years ago kpitz23 • 0
0
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1
reply
1.2k
views
phyloseq biom json format conversion needed to hdf5 format for qiime
biom json hdf5 qiime phyloseq
updated 4.9 years ago by ▴ 540 • written 4.9 years ago by • 0
0
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1
reply
1.3k
views
phyloseq merge_samples attempt to set rownames on an object with no dimensions
phyloseq merge_samples rownames error
5.0 years ago newmanss • 0
0
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3
replies
931
views
DESeq2 blocking by condition over time
deseq2 phyloseq time course
5.0 years ago akp • 0
0
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0
replies
545
views
displaying network from microbial count data
phyloseq
5.1 years ago chrisclarkson100 ▴ 50
0
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0
replies
461
views
Testing for OTUs with negatively correlated abundances/occurrences
phyloseq
5.2 years ago am39 • 0
0
votes
3
replies
1.3k
views
Newer version of DESeq2 gives different results
deseq2 phyloseq
updated 5.3 years ago by 34k • written 5.3 years ago by • 0
0
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1
reply
555
views
Aditional undesired sample
phyloseq
5.5 years ago sanrrone • 0
3
votes
2
replies
1.6k
views
DESEQ2 (R) design/contrast formula questions
deseq2 phyloseq multiple factor design paired samples
updated 5.5 years ago by ▴ 20 • written 5.5 years ago by ▴ 10
2
votes
2
replies
3.7k
views
Interpretation of intercept-only model (~1) in DESeq2
deseq2 phyloseq
updated 5.5 years ago by 34k • written 5.5 years ago by ▴ 10
50 results • Page 1 of 1
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Answer: Undefined columns error R cytometry analysis by Jiang, Mike ★ 1.3k
I see you are trying to fill the missing transform info to `gs_bcell_auto` , which is a hack, but since you seems to know what you are doin…
Comment: how to get MFI stats from data by Jiang, Mike ★ 1.3k
Can you grant the public caccess to you fcs to reproduce your issue?
Answer: Getting a dataset that only contains the flow data within the gated area by Jiang, Mike ★ 1.3k
You didn't post your example code, so here is my best guess of your workflow > library(flowCore) > library(flowWorkspace) …
Comment: Diffbind dba.plotProfile attempt to select less than one element in OneIndex by bhanratt • 0
``` > DBA 10 Samples, 31953 sites in matrix: ID Tissue Factor Condition Replicate Reads FRiP 1 58 1 H3K4me3 AD …
Answer: Warning messages on Apple M1 BigSur by Vincent J. Carey, Jr. 6.5k
We are not producing M1 binaries at this time. If you use the intel version of R under Rosetta 2 you can use the intel mac binaries.
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Comment: Use of coef() as a measure of effect size in a multiple regression using DESeq2
Answer: Log fold change interpretation of time series with Wald test
A: gviz: name of tracks disappeas
Answer: Degust: what normalization method does it use
Answer: ylim and xlim in Enhanced Volcano
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