Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
PHYLOSEQ
•
reset
0
votes
2
replies
76
views
I cannot install "microbiome"
GenomeInfoDbData
microbiome
phyloseq
3 days ago • updated 2 days ago
kikiki
• 0
0
votes
1
reply
107
views
error installing phyloseq
phyloseq
updated 8 weeks ago by
shepherl
3.2k • written 8 weeks ago by
Ezra
• 0
0
votes
3
replies
229
views
Controversial DESEQ2 results
phyloseq
DESeq2
updated 9 weeks ago by
Michael Love
37k • written 9 weeks ago by
Stephan
• 0
0
votes
0
replies
79
views
Association between ohylum and genus on microbiome data sets.
phyloseq
3 months ago
Edmond
• 0
0
votes
0
replies
251
views
How to pool phyloseq data?
phyloseq
r
updated 4 months ago by
Michael Love
37k • written 4 months ago by
strep
• 0
0
votes
4
replies
330
views
Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), : key 51 (char '3') not in lookup table
Biostrings
phyloseq
updated 4 months ago by
James W. MacDonald
60k • written 5 months ago by
Eman
• 0
0
votes
1
reply
223
views
Deseq workflow for phyloseq object and complicated data structure?
phyloseq
DESeq2
updated 6 months ago by
Michael Love
37k • written 6 months ago by
dschnitzler
• 0
0
votes
4
replies
498
views
Cannot install Phyloseq and dada2
GenomeInfoDbData
phyloseq
dada2
6 months ago
ymtan
• 0
0
votes
1
reply
185
views
Error in 'differential_abundance'
phyloseq
devtools
updated 7 months ago by
Michael Love
37k • written 7 months ago by
strep
• 0
0
votes
2
replies
309
views
convert default phylip to sequential phylip
phyloseq
Phylogenetics
written 11 months ago by
memy
• 0
0
votes
0
replies
266
views
Construct a phyloseq object directly from the dada2 outputs
phyloseq
dada2
11 months ago
Manijeh
• 0
0
votes
3
replies
322
views
DESeq2: difficulty with contrasts and main effects
DESeq2
phyloseq
contrasts
updated 12 months ago by
Kevin Blighe
3.6k • written 12 months ago by
Mir
• 0
0
votes
5
replies
2.2k
views
Problems with installation of 'phyloseq
phyloseq
updated 12 months ago by
Kevin Blighe
3.6k • written 12 months ago by
Ina
• 0
0
votes
1
reply
266
views
Purpose of seqtabNoC
phyloseq
updated 13 months ago by
Kevin Blighe
3.6k • written 13 months ago by
klltnq
• 0
0
votes
0
replies
236
views
Construct Phylogenetic Tree
phyloseq
13 months ago
klltnq
• 0
0
votes
0
replies
218
views
Code Issue
phyloseq
13 months ago
klltnq
• 0
0
votes
3
replies
289
views
Installing Packages repeatedly
phyloseq
updated 13 months ago by
Kevin Blighe
3.6k • written 13 months ago by
klltnq
• 0
0
votes
1
reply
852
views
Import MetaPhlAn3 to Phyloseq
Metaphlan3
Metagenomics
phyloseq
updated 13 months ago by
Levi Waldron
1.1k • written 13 months ago by
Saraswati
• 0
1
vote
1
reply
1.3k
views
Setting up bioconductor on a Linux server using conda
dada2
conda
phyloseq
updated 16 months ago by
James W. MacDonald
60k • written 16 months ago by
Daniel
• 0
1
vote
3
replies
394
views
How to assign random effect factor in DESeq2 desing?
StatisticalMethod
DESeq2
phyloseq
updated 17 months ago by
Michael Love
37k • written 17 months ago by
zardbid
• 0
4
votes
3
replies
478
views
Paired-test between two groups within a condition after phyloseq_to_deseq2
DESeq2
phyloseq
updated 18 months ago by
Michael Love
37k • written 18 months ago by
trichorico
▴ 10
0
votes
0
replies
499
views
Co-occurrence Network Analysis between Algae and Bacteria
igraph
networkanalysis
Phylogenetics
phyloseq
19 months ago
Chantel
• 0
1
vote
2
replies
1.3k
views
Bioconductor install error
phyloseq
Bioconductor
20 months ago
Tess
• 0
2
votes
2
replies
631
views
Bioconductor phyloseq taking forever to install?
Bioconductor
phyloseq
21 months ago
garfield320
▴ 30
0
votes
1
reply
583
views
Can I use pseudocounts for differential abundance of OTUs?
metagenomics
deseq2
PHYLOSEQ
updated 2.0 years ago by
Michael Love
37k • written 2.0 years ago by
dc
• 0
0
votes
2
replies
559
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
2.1 years ago
jaiber.solano.i
• 0
0
votes
3
replies
402
views
Nested design- phyloseq_to_deseq
deseq2
Phyloseq
Nested
updated 2.4 years ago by
Michael Love
37k • written 2.4 years ago by
mpuli011
• 0
0
votes
2
replies
1.9k
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 2.6 years ago by
Martin Morgan
25k • written 2.6 years ago by
crgarcia
• 0
0
votes
0
replies
423
views
Problems with creating phyloseq bar plots from a table with species data
phyloseq
microbiome analysis
3.5 years ago
lm795
▴ 10
0
votes
2
replies
538
views
Phyloseq to DESeq2
deseq2
phyloseq
updated 3.5 years ago by
Michael Love
37k • written 3.5 years ago by
staffordvigors
• 0
0
votes
1
reply
855
views
Import_biom with tree problem
phyloseq
mothur
16s
3.8 years ago
andrebolerbarros
▴ 10
5
votes
11
replies
1.9k
views
Error while installing Phyloseq using biocLite
bioclite
phyloseq
install error
3.8 years ago
khp
▴ 30
0
votes
9
replies
1.4k
views
DESEQ2 / Phyloseq contrasts no longer work as before following update
deseq2
phyloseq
3.9 years ago
eoin
• 0
0
votes
1
reply
477
views
Invalid class DESeqDataSet object with Phyloseq
deseq2
phyloseq
updated 4.0 years ago by
Michael Love
37k • written 4.0 years ago by
amgodogma
▴ 10
0
votes
1
reply
893
views
Install package phyloseq
installation
phyloseq
updated 4.4 years ago by
Martin Morgan
25k • written 4.4 years ago by
layeb
• 0
0
votes
1
reply
852
views
tip_glom and annotations?
ggtree
treeio
phyloseq
annotation
tip_glom
updated 4.5 years ago by
Guangchuang Yu
★ 1.2k • written 4.5 years ago by
werdnus
• 0
1
vote
1
reply
852
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2
R
microbiome
phyloseq
qiime
updated 4.7 years ago by
Michael Love
37k • written 4.7 years ago by
ssingh59
• 0
1
vote
8
replies
3.6k
views
Cannot read Biom file
r
biomformat
phyloseq
updated 4.8 years ago by
Axel Klenk
▴ 990 • written 4.8 years ago by
channen1221
• 0
0
votes
0
replies
722
views
Problem with ade4 when upgrading to Rstudio 1.1 and OpenR 3.4
phyloseq
installation
ade4
macos
4.8 years ago
sprague
• 0
2
votes
2
replies
2.0k
views
DESeq2 iterative size factor normalization did not converge
deseq2
microbiome
phyloseq
updated 4.9 years ago by
Michael Love
37k • written 4.9 years ago by
couchc
• 0
0
votes
1
reply
779
views
phyloseq heatmap blank after multiple package updates
phyloseq
heatmap
updated 4.9 years ago by
Wolfgang Huber
13k • written 4.9 years ago by
newmanss
• 0
1
vote
3
replies
1.2k
views
Error bars on DESeq2 visuals
deseq2
metagenomics
phyloseq
ggplot2
5.0 years ago
lauren.czaplicki
• 0
0
votes
1
reply
958
views
Phyloseq to DESeq2 with multiple variables
deseq2
phyloseq
multiple time points
updated 5.1 years ago by
Michael Love
37k • written 5.1 years ago by
campbell87
• 0
0
votes
0
replies
793
views
Phylogenetic tree from marker genes
ape
phyloseq
dist
metagenomics
5.3 years ago
David
▴ 860
1
vote
1
reply
2.4k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome
normalization
variancestabilizingtransformation
phyloseq
5.3 years ago
stats134711
• 0
0
votes
1
reply
1.4k
views
ggtree facet_plot question using geom_boxplot to plot abundance data corresponding to tree tips
ggtree
ggplot2
phyloseq
geom_boxplot
facet_plot
updated 5.4 years ago by
Guangchuang Yu
★ 1.2k • written 5.4 years ago by
matthew.wipperman
• 0
2
votes
2
replies
1.1k
views
DESeq2 in phyloseq
deseq2
phyloseq
5.4 years ago
sarahmacdonald86
• 0
0
votes
2
replies
1.3k
views
Controlling colours assigned to order in DeSeq2 plot in phyloseq
phyloseq
color
ggplot2
updated 5.4 years ago by
Michael Love
37k • written 5.4 years ago by
sarahmacdonald86
• 0
1
vote
2
replies
981
views
rlogTransformation vs getVarianceStabilizedData
deseq2
r
phyloseq
updated 5.7 years ago by
Michael Love
37k • written 5.7 years ago by
fabian.roger08
▴ 10
0
votes
0
replies
1.5k
views
Error with phyloseq R package with Conda install
software error
phyloseq
anaconda
5.8 years ago
kpitz23
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: OPLS-DA: confidence interval for accuracy metric
by
etienne.thevenot
▴ 20
- The bootstrapping approach can be used to compute the CIs: see here for an example: Mendez et al. (2019). « A comparative evaluation …
Comment: Data input for aracne2regulon function in viper package
by
xlal
• 0
You are right!And may be we should check the gene symbols cause when I open the expression matrix in EXCEL,it will change some genes into m…
Comment: unable to install.packages("spatialLIBD")
by
Leonardo Collado Torres
▴ 1000
All the solutions Lori proposed are valid. The `STexampleData` package I think has only 1 of our samples (see https://bioconductor.org/pack…
Answer: how to use Rsamtools to parse extra fields from STAR alignment
by
Martin Morgan
25k
The 'extra columns' are called 'tags' in the SAM specification. Following the documentation `?ScanBamParam` you should add `tag = "NH"`. Se…
Comment: DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscrip
by
Delta._.43
▴ 10
Yes, indeed it is the same error. Here are the first few lines of my count file. ``` "ENSG00000000003":"001" 0 "ENSG00000000003":"002" 1032…
Votes
Answer: spot- vs cell-level data access
Answer: unable to install.packages("spatialLIBD")
Comment: unable to install.packages("spatialLIBD")
error running UniProt.ws
Answer: DEXSeq errors "Error in scan( line ... did not have 3 elements" and "Error in FU
Awards
• All
Popular Question
to
Alejandro Reyes
★ 1.8k
Popular Question
to
Leonardo Collado Torres
▴ 1000
Scholar
to
ATpoint
★ 1.4k
Scholar
to
voogd.o
▴ 10
Popular Question
to
Bumble
▴ 10
Locations
• All
Netherlands,
just now
Zheng Zhou,
5 minutes ago
WEHI, Melbourne, Australia,
5 minutes ago
Belgium,
7 minutes ago
United Kingdom,
9 minutes ago
Traffic: 423 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6