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dada2
•
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0
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2
replies
663
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Issue when attempting to use output from DECIPHER IDtaxa (pr2 V5) with dada2/phyloseq
DECIPHER
taxonomyassignment
phyloseq
dada2
Pr2V5
updated 8 weeks ago by
Daniel
• 0 • written 4 months ago by
Maggie
• 0
0
votes
4
replies
1.5k
views
Trouble Installing DADA2 (warning: R new user)
dada2
updated 10 months ago by
shepherl
4.1k • written 10 months ago by
schott01
• 0
0
votes
2
replies
942
views
Species level information couldn't find with DADA2 bioconductor package
Metagenomics
dada2
MicrobiomeData
10 months ago • updated 8 months ago
abhisek001
• 0
0
votes
1
reply
633
views
Problem in execuation of filterAndTrim command in DADA2
Bioconductor
dada2
12 months ago • updated 10 months ago
abhisek001
• 0
0
votes
0
replies
629
views
is Dada2 biased toward a particular sequence ?
virology
dada2
amplican
Sequencing
RNASeq
19 months ago
Sara
• 0
0
votes
0
replies
711
views
Using DADA2 for finding viral sequence variants
VariantDetection
dada2
RNASeq
19 months ago
Sara
• 0
2
votes
2
replies
771
views
Broken UNITE 9.0 link (General FASTA Release)
dada2
UNITE
21 months ago
GlycineMax
• 0
0
votes
14
replies
3.0k
views
Trouble downloading dada2
dada
dada2
2.3 years ago
elliottchon97
• 0
0
votes
3
replies
1.5k
views
Problem with multiple sequence alignment using AlignSeqs
R
dada2
DECIPHER
updated 2.4 years ago by
Erik Wright
▴ 150 • written 2.5 years ago by
Nelli
• 0
0
votes
2
replies
1.3k
views
Microbiome 16S amplicon analysis in dada2
bioinformatics
DADA2
2.7 years ago
anasjamshed1994
• 0
1
vote
3
replies
1.6k
views
Assign taxonomy is not working
Assigntaxonomy
dada2
updated 3.1 years ago by
shepherl
4.1k • written 3.1 years ago by
safiq713
• 0
27
votes
13
replies
19k
views
problems about installation of package ‘Rhtslib’, ‘Rsamtools’ ,‘GenomicAlignments’ , ‘ShortRead’ on macOS Big Sur using R 4.1.0
dada2
updated 2.3 years ago by
Yoon Young
• 0 • written 4.0 years ago by
lh290
▴ 60
0
votes
4
replies
2.4k
views
Cannot install Phyloseq and dada2
GenomeInfoDbData
phyloseq
dada2
3.3 years ago
ymtan
• 0
0
votes
0
replies
1.1k
views
Construct a phyloseq object directly from the dada2 outputs
phyloseq
dada2
3.7 years ago
Manijeh
• 0
0
votes
0
replies
1.3k
views
dada2 (derepFastaq function) 'Calloc' could not allocate memory (1000000 of 16 bytes) in r version 4.1.0
dada2
3.8 years ago
Yoan
• 0
0
votes
5
replies
2.9k
views
Do DECIPHER:IdTaxa / dada2::assignTaxonomy work with ambigious reference training set?
decipher
dada2
updated 4.0 years ago by
fabian.roger08
▴ 10 • written 5.3 years ago by
fabian.roger
• 0
0
votes
1
reply
1.0k
views
FDR Correction
dada2
Metagenomics
DESeq2
updated 4.0 years ago by
Michael Love
43k • written 4.0 years ago by
GlycineMax
• 0
4
votes
8
replies
5.1k
views
Is there a different way to generate a tree for phyloseq object
r
dada2
Bioconductor
updated 4.0 years ago by
Axel Klenk
★ 1.1k • written 4.0 years ago by
mschmidt
▴ 10
0
votes
0
replies
1.3k
views
DECIPHER Package on dada2 -Implementing Silva_metaxa2 training set from qza file into a fastq.gz/.Rdata
DECIPHER
dada2
4.1 years ago
anrongloh
• 0
1
vote
1
reply
5.0k
views
Setting up bioconductor on a Linux server using conda
dada2
conda
phyloseq
updated 4.1 years ago by
James W. MacDonald
68k • written 4.1 years ago by
Daniel
• 0
0
votes
0
replies
1.5k
views
from raw reads ASV table - dada2 - small number of merged pairs
dada2
515F - 806Rd
5.2 years ago
beginner87
• 0
0
votes
1
reply
2.3k
views
Error: record does not start with '@'
DADA2
.fq
updated 6.4 years ago by
James W. MacDonald
68k • written 6.4 years ago by
mafusa20
• 0
0
votes
1
reply
1.3k
views
Cannot Update Biostrings to Latest Version
dada2
biostrings
updated 6.8 years ago by
James W. MacDonald
68k • written 6.8 years ago by
gradypierroz
• 0
4
votes
4
replies
3.1k
views
Using DADA2 output for DESeq2
deseq2
dada2
updated 7.2 years ago by
benjamin.j.callahan
▴ 50 • written 7.2 years ago by
blastzone.heimerdinger
▴ 20
0
votes
1
reply
2.0k
views
dada2 unavailable for R 3.4.1
bioconductor
R
dada2
updated 7.7 years ago by
daniel.vantwisk
▴ 50 • written 7.7 years ago by
rggriggs
• 0
1
vote
7
replies
20k
views
Dada2 and GenomeInfoDbData installation
dada2
GenomeInfoDbData
updated 7.9 years ago by
jiangjing_ing
• 0 • written 8.0 years ago by
navlern
• 0
26 results • Page
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Comment: Check removeBatchEffect effectiveness
by
massimo
• 0
Yes, I still get the warning, so there is confounding apparently. However, the resulting adjusted matrix is quite different than before and…
Answer: Limma trend with limpa
by
Gordon Smyth
52k
Dear Alejandro, Thanks for your interest. No, one does not set `trend=TRUE` when running eBayes() after dpcDE(). The variance trends are …
Comment: Check removeBatchEffect effectiveness
by
Gordon Smyth
52k
Both of your matrices, `design_batcheffects` and `design_timepoint`, span the intercept term, which will cause a warning about NA coefficie…
Comment: DiffBind - question on the use of filtered or unfiltered input data
by
sloperun3az
• 0
Your essay was beneficial to me, and I found it to be very useful. Thank you for writing it. You give a wealth of knowledge that is not onl…
Comment: compute_fasta_digest does not match Salmon index hash
by
sloperun3az
• 0
The people who are reading your work are not taken into consideration, even though you appear to have a solid understanding of the subject …
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Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
A: what should I do with many zero counts from Salmon quantification
Comment: parameters of filterByExpr
GAlignments Cigar to GRanges
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