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dada2
•
reset
0
votes
14
replies
2.0k
views
Trouble downloading dada2
dada
dada2
14 months ago
elliottchon97
• 0
27
votes
13
replies
16k
views
problems about installation of package ‘Rhtslib’, ‘Rsamtools’ ,‘GenomicAlignments’ , ‘ShortRead’ on macOS Big Sur using R 4.1.0
dada2
updated 14 months ago by
Yoon Young
• 0 • written 2.9 years ago by
lh290
▴ 60
4
votes
8
replies
3.8k
views
Is there a different way to generate a tree for phyloseq object
r
dada2
Bioconductor
updated 3.0 years ago by
Axel Klenk
★ 1.0k • written 3.0 years ago by
mschmidt
▴ 10
1
vote
7
replies
17k
views
Dada2 and GenomeInfoDbData installation
dada2
GenomeInfoDbData
updated 6.8 years ago by
jiangjing_ing
• 0 • written 6.9 years ago by
navlern
• 0
0
votes
5
replies
2.2k
views
Do DECIPHER:IdTaxa / dada2::assignTaxonomy work with ambigious reference training set?
decipher
dada2
updated 2.9 years ago by
fabian.roger08
▴ 10 • written 4.2 years ago by
fabian.roger
• 0
4
votes
4
replies
2.5k
views
Using DADA2 output for DESeq2
deseq2
dada2
updated 6.1 years ago by
benjamin.j.callahan
▴ 50 • written 6.1 years ago by
blastzone.heimerdinger
▴ 20
0
votes
4
replies
1.7k
views
Cannot install Phyloseq and dada2
GenomeInfoDbData
phyloseq
dada2
2.3 years ago
ymtan
• 0
0
votes
3
replies
1.0k
views
Problem with multiple sequence alignment using AlignSeqs
R
dada2
DECIPHER
updated 16 months ago by
Erik Wright
▴ 150 • written 16 months ago by
Nelli
• 0
1
vote
3
replies
1.2k
views
Assign taxonomy is not working
Assigntaxonomy
dada2
updated 2.0 years ago by
shepherl
3.8k • written 2.0 years ago by
safiq713
• 0
2
votes
2
replies
419
views
Broken UNITE 9.0 link (General FASTA Release)
dada2
UNITE
8 months ago
GlycineMax
• 0
0
votes
2
replies
813
views
Microbiome 16S amplicon analysis in dada2
bioinformatics
DADA2
20 months ago
anasjamshed1994
• 0
1
vote
1
reply
3.6k
views
Setting up bioconductor on a Linux server using conda
dada2
conda
phyloseq
updated 3.1 years ago by
James W. MacDonald
65k • written 3.1 years ago by
Daniel
• 0
0
votes
1
reply
1.7k
views
dada2 unavailable for R 3.4.1
bioconductor
R
dada2
updated 6.7 years ago by
daniel.vantwisk
▴ 50 • written 6.7 years ago by
rggriggs
• 0
0
votes
1
reply
1.9k
views
Error: record does not start with '@'
DADA2
.fq
updated 5.3 years ago by
James W. MacDonald
65k • written 5.3 years ago by
mafusa20
• 0
0
votes
1
reply
756
views
FDR Correction
dada2
Metagenomics
DESeq2
updated 2.9 years ago by
Michael Love
41k • written 2.9 years ago by
GlycineMax
• 0
0
votes
1
reply
990
views
Cannot Update Biostrings to Latest Version
dada2
biostrings
updated 5.7 years ago by
James W. MacDonald
65k • written 5.7 years ago by
gradypierroz
• 0
0
votes
0
replies
942
views
DECIPHER Package on dada2 -Implementing Silva_metaxa2 training set from qza file into a fastq.gz/.Rdata
DECIPHER
dada2
3.0 years ago
anrongloh
• 0
0
votes
0
replies
318
views
is Dada2 biased toward a particular sequence ?
virology
dada2
amplican
Sequencing
RNASeq
6 months ago
Sara
• 0
0
votes
0
replies
758
views
Construct a phyloseq object directly from the dada2 outputs
phyloseq
dada2
2.7 years ago
Manijeh
• 0
0
votes
0
replies
1.0k
views
from raw reads ASV table - dada2 - small number of merged pairs
dada2
515F - 806Rd
4.1 years ago
beginner87
• 0
0
votes
0
replies
966
views
dada2 (derepFastaq function) 'Calloc' could not allocate memory (1000000 of 16 bytes) in r version 4.1.0
dada2
2.7 years ago
Yoan
• 0
0
votes
0
replies
315
views
Using DADA2 for finding viral sequence variants
VariantDetection
dada2
RNASeq
6 months ago
Sara
• 0
22 results • Page
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Comment: Finding DEGs by using edgeR
by
Gordon Smyth
50k
Filtering (removing lowly expressed genes) is separate to normalization. It isn't clear why not subsetting would cause any difficulty. It …
Comment: How to make DGEList and design matrix by edgeR package
by
prity6459
• 0
Thank you for your suggestion. Yes, I have made DGEList and design matrix in my script. But I was not entirely confident while making thos…
Comment: Finding DEGs by using edgeR
by
prity6459
• 0
Hello Gordon, Thanks for your response. By normalization, I meant that I have already removed lowly expressed genes from my count matrix. …
Answer: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
It doesn't seem to me that there is necessarily any problem with the analysis. You say that there are "too many low-reads" but actually th…
Answer: How to make DGEList and design matrix by edgeR package
by
Gordon Smyth
50k
Your question is curious because you showed code that made a DGEList and design matrix in your previous post just 15 hours ago. Please h…
Votes
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
Comment: DEXSeq DEXSeqDataSet count matrix duplication
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