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Showing :
phyloseq
•
reset
2
votes
1
reply
857
views
Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq
microbiome
Software
updated 6 months ago by
ATpoint
★ 3.9k • written 6 months ago by
HULFRED
▴ 10
0
votes
0
replies
321
views
Try to understand better how to set out an effective sample size within the MetagenomSeq package in microbiome ?
Metagenomics
metagenomeSeq
microbiome
phyloseq
microbiomeDataSets
7 months ago
Mohamed
▴ 30
0
votes
2
replies
519
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
written 9 months ago by
abhisek001
• 0
0
votes
6
replies
1.3k
views
convert default phylip to sequential phylip
phyloseq
Phylogenetics
updated 10 months ago by
yrkkhdesiserials
• 0 • written 2.6 years ago by
memy
• 0
1
vote
1
reply
2.2k
views
does anyone how to create rarefaction curves from a phyloseq object?
phyloseq
Phylogenetics
updated 12 months ago by
RMiller
▴ 10 • written 12 months ago by
kevin
• 0
0
votes
3
replies
1.5k
views
I cannot install "microbiome"
GenomeInfoDbData
microbiome
phyloseq
updated 19 months ago by
Marcel Ramos
680 • written 19 months ago by
kikiki
• 0
0
votes
1
reply
618
views
error installing phyloseq
phyloseq
updated 21 months ago by
shepherl
3.8k • written 21 months ago by
Ezra
• 0
0
votes
3
replies
829
views
Controversial DESEQ2 results
phyloseq
DESeq2
updated 21 months ago by
Michael Love
41k • written 21 months ago by
Stephan
• 0
0
votes
0
replies
458
views
Association between ohylum and genus on microbiome data sets.
phyloseq
22 months ago
Edmond
• 0
0
votes
0
replies
1.3k
views
How to pool phyloseq data?
phyloseq
r
updated 24 months ago by
Michael Love
41k • written 24 months ago by
strep
• 0
0
votes
4
replies
1.7k
views
Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings
phyloseq
updated 2.0 years ago by
James W. MacDonald
65k • written 2.0 years ago by
Eman
• 0
0
votes
1
reply
728
views
Deseq workflow for phyloseq object and complicated data structure?
phyloseq
DESeq2
updated 2.2 years ago by
Michael Love
41k • written 2.2 years ago by
dschnitzler
• 0
0
votes
4
replies
1.7k
views
Cannot install Phyloseq and dada2
GenomeInfoDbData
phyloseq
dada2
2.2 years ago
ymtan
• 0
0
votes
1
reply
648
views
Error in 'differential_abundance'
phyloseq
devtools
updated 2.2 years ago by
Michael Love
41k • written 2.2 years ago by
strep
• 0
0
votes
0
replies
734
views
Construct a phyloseq object directly from the dada2 outputs
phyloseq
dada2
2.6 years ago
Manijeh
• 0
0
votes
3
replies
944
views
DESeq2: difficulty with contrasts and main effects
DESeq2
phyloseq
contrasts
updated 2.6 years ago by
Kevin Blighe
★ 3.9k • written 2.6 years ago by
Mir
• 0
0
votes
5
replies
6.1k
views
Problems with installation of 'phyloseq
phyloseq
updated 2.6 years ago by
Kevin Blighe
★ 3.9k • written 2.6 years ago by
Ina
• 0
0
votes
1
reply
661
views
Purpose of seqtabNoC
phyloseq
updated 2.7 years ago by
Kevin Blighe
★ 3.9k • written 2.7 years ago by
klltnq
• 0
0
votes
0
replies
692
views
Construct Phylogenetic Tree
phyloseq
2.7 years ago
klltnq
• 0
0
votes
0
replies
592
views
Code Issue
phyloseq
2.7 years ago
klltnq
• 0
0
votes
3
replies
737
views
Installing Packages repeatedly
phyloseq
updated 2.7 years ago by
Kevin Blighe
★ 3.9k • written 2.7 years ago by
klltnq
• 0
0
votes
1
reply
2.1k
views
Import MetaPhlAn3 to Phyloseq
Metaphlan3
Metagenomics
phyloseq
updated 2.7 years ago by
Levi Waldron
★ 1.1k • written 2.7 years ago by
Saraswati
• 0
1
vote
1
reply
3.5k
views
Setting up bioconductor on a Linux server using conda
dada2
conda
phyloseq
updated 3.0 years ago by
James W. MacDonald
65k • written 3.0 years ago by
Daniel
• 0
1
vote
3
replies
1.0k
views
How to assign random effect factor in DESeq2 desing?
StatisticalMethod
DESeq2
phyloseq
updated 3.1 years ago by
Michael Love
41k • written 3.1 years ago by
zardbid
• 0
4
votes
3
replies
1.1k
views
Paired-test between two groups within a condition after phyloseq_to_deseq2
DESeq2
phyloseq
updated 3.1 years ago by
Michael Love
41k • written 3.1 years ago by
trichorico
▴ 10
0
votes
0
replies
1.0k
views
Co-occurrence Network Analysis between Algae and Bacteria
igraph
networkanalysis
Phylogenetics
phyloseq
3.2 years ago
Chantel
• 0
1
vote
2
replies
2.2k
views
Bioconductor install error
phyloseq
Bioconductor
3.3 years ago
Tess
• 0
2
votes
2
replies
1.5k
views
Bioconductor phyloseq taking forever to install?
Bioconductor
phyloseq
3.4 years ago
garfield320
▴ 30
0
votes
1
reply
1.1k
views
Can I use pseudocounts for differential abundance of OTUs?
metagenomics
deseq2
PHYLOSEQ
updated 3.6 years ago by
Michael Love
41k • written 3.6 years ago by
dc
• 0
0
votes
2
replies
1.8k
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
3.7 years ago
jaiber.solano.i
• 0
0
votes
3
replies
965
views
Nested design- phyloseq_to_deseq
deseq2
Phyloseq
Nested
updated 4.0 years ago by
Michael Love
41k • written 4.0 years ago by
mpuli011
• 0
0
votes
2
replies
2.8k
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 4.2 years ago by
Martin Morgan
25k • written 4.2 years ago by
crgarcia
• 0
0
votes
0
replies
791
views
Problems with creating phyloseq bar plots from a table with species data
phyloseq
microbiome analysis
5.1 years ago
lm795
▴ 10
0
votes
2
replies
943
views
Phyloseq to DESeq2
deseq2
phyloseq
updated 5.2 years ago by
Michael Love
41k • written 5.2 years ago by
staffordvigors
• 0
0
votes
1
reply
1.5k
views
Import_biom with tree problem
phyloseq
mothur
16s
5.4 years ago
andrebolerbarros
▴ 30
5
votes
11
replies
2.7k
views
Error while installing Phyloseq using biocLite
bioclite
phyloseq
install error
5.4 years ago
khp
▴ 30
0
votes
9
replies
2.4k
views
DESEQ2 / Phyloseq contrasts no longer work as before following update
deseq2
phyloseq
5.5 years ago
eoin
• 0
0
votes
1
reply
799
views
Invalid class DESeqDataSet object with Phyloseq
deseq2
phyloseq
updated 5.6 years ago by
Michael Love
41k • written 5.6 years ago by
amgodogma
▴ 10
0
votes
1
reply
1.6k
views
Install package phyloseq
installation
phyloseq
updated 6.0 years ago by
Martin Morgan
25k • written 6.0 years ago by
layeb
• 0
0
votes
1
reply
1.5k
views
tip_glom and annotations?
ggtree
treeio
phyloseq
annotation
tip_glom
updated 6.1 years ago by
Guangchuang Yu
★ 1.2k • written 6.1 years ago by
werdnus
• 0
1
vote
1
reply
1.3k
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2
R
microbiome
phyloseq
qiime
updated 6.3 years ago by
Michael Love
41k • written 6.3 years ago by
ssingh59
• 0
1
vote
8
replies
5.7k
views
Cannot read Biom file
r
biomformat
phyloseq
updated 6.4 years ago by
Axel Klenk
▴ 990 • written 6.4 years ago by
channen1221
• 0
0
votes
0
replies
1.2k
views
Problem with ade4 when upgrading to Rstudio 1.1 and OpenR 3.4
phyloseq
installation
ade4
macos
6.4 years ago
sprague
• 0
3
votes
2
replies
3.2k
views
DESeq2 iterative size factor normalization did not converge
deseq2
microbiome
phyloseq
updated 6.5 years ago by
Michael Love
41k • written 6.5 years ago by
couchc
• 0
0
votes
1
reply
1.3k
views
phyloseq heatmap blank after multiple package updates
phyloseq
heatmap
updated 6.5 years ago by
Wolfgang Huber
★ 13k • written 6.5 years ago by
newmanss
• 0
1
vote
3
replies
1.8k
views
Error bars on DESeq2 visuals
deseq2
metagenomics
phyloseq
ggplot2
6.6 years ago
lauren.czaplicki
• 0
0
votes
1
reply
1.5k
views
Phyloseq to DESeq2 with multiple variables
deseq2
phyloseq
multiple time points
updated 6.7 years ago by
Michael Love
41k • written 6.7 years ago by
campbell87
• 0
0
votes
0
replies
1.3k
views
Phylogenetic tree from marker genes
ape
phyloseq
dist
metagenomics
6.9 years ago
David
▴ 860
1
vote
1
reply
3.4k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome
normalization
variancestabilizingtransformation
phyloseq
6.9 years ago
stats134711
• 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 7.0 years ago by
Guangchuang Yu
★ 1.2k • written 7.0 years ago by
matthew.wipperman
• 0
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Replies
Comment: DEG Filtering
by
Gordon Smyth
50k
RMA normalization is good but batch correction using NOISeq isn't right. Data shouldn't be batch corrected before the limma analysis and NO…
Answer: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
by
snijesh
▴ 20
You can try: using `read.delim` or `fread`. ``` my_maf = data.table::fread("path/to/maf/sample.maf") my_maf = read.maf(maf = my_maf) …
Comment: DEG Filtering
by
Amit
• 0
Hi Gordon, Thank you for your response and advice. I want to analyze Dataset GSE18090 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) whic…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
Gordon Smyth
50k
Yes, that is a quote from [A guide to creating design matrices for gene expression experiments](https://bioconductor.org/packages/release/w…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
JKim
• 0
Thank you. I think I found why the order matters. > Although an intercept-free design matrix has been coded using the 0+ notation, the in…
Votes
C: How to check that the reads in two fastq files are in the same order
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
Answer: Need help with creating and plotting temporal clustering analysis of DEGs
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
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