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qiime
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2
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9
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19k
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Error in file(con, “r”) : cannot open the connection
r
phyloseq
import_biom
otu
qiime
updated 8.5 years ago by
mcmurdie
▴ 20 • written 8.5 years ago by
moanam
• 0
2
votes
1
reply
1.6k
views
Metagenome seq errors using biom (1.3) file
metagenomeseq
qiime
biom
updated 7.7 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 7.7 years ago by
dr.richrodrigues
• 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
Bernd Fischer
▴ 550 • written 7.5 years ago by
newmanss
• 0
1
vote
1
reply
2.3k
views
QIIME, R and bioconducter
R
qiime
updated 7.1 years ago by
James W. MacDonald
65k • written 7.1 years ago by
trichter
• 0
1
vote
2
replies
989
views
QIIME Differential abundance on multiple studies
deseq2
qiime
updated 6.5 years ago by
Michael Love
41k • written 6.5 years ago by
syafiqkamarulazman
• 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
Michael Love
41k • written 6.4 years ago by
ssingh59
• 0
0
votes
1
reply
807
views
DESeq2 intstallation error on fedora
deseq2
R
fedora
qiime
updated 5.7 years ago by
Michael Love
41k • written 5.7 years ago by
kperlejewski
• 0
7 results • Page
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Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param
by
russ.bainer
▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Chris
• 0
Hi Robert, If I don't want to use all pathway in c2 gene set but only a few pathways of interested, how can I do that? So we try to get a …
Comment: How to retrieve detailed regression results from deseq2
by
Weiqian
▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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