Showing : dada2 • reset
1
vote
7
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17k
views
Dada2 and GenomeInfoDbData installation
dada2 GenomeInfoDbData
updated 6.8 years ago by • 0 • written 6.9 years ago by • 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 • 0 • written 2.9 years ago by ▴ 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 ★ 1.0k • written 3.0 years ago by ▴ 10
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 65k • written 3.1 years ago by • 0
4
votes
4
replies
2.5k
views
Using DADA2 output for DESeq2
deseq2 dada2
updated 6.2 years ago by ▴ 50 • written 6.2 years ago by ▴ 20
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 ▴ 10 • written 4.2 years ago by • 0
0
votes
14
replies
2.0k
views
Trouble downloading dada2
dada dada2
14 months ago elliottchon97 • 0
0
votes
1
reply
1.9k
views
Error: record does not start with '@'
DADA2 .fq
updated 5.3 years ago by 65k • written 5.3 years ago by • 0
0
votes
4
replies
1.8k
views
Cannot install Phyloseq and dada2
GenomeInfoDbData phyloseq dada2
2.3 years ago ymtan • 0
0
votes
1
reply
1.7k
views
dada2 unavailable for R 3.4.1
bioconductor R dada2
updated 6.7 years ago by ▴ 50 • written 6.7 years ago by • 0
1
vote
3
replies
1.2k
views
Assign taxonomy is not working
Assigntaxonomy dada2
updated 2.0 years ago by 3.8k • written 2.0 years ago by • 0
0
votes
3
replies
1.0k
views
Problem with multiple sequence alignment using AlignSeqs
R dada2 DECIPHER
updated 16 months ago by ▴ 150 • written 16 months ago by • 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
1
reply
995
views
Cannot Update Biostrings to Latest Version
dada2 biostrings
updated 5.7 years ago by 65k • written 5.7 years ago by • 0
0
votes
0
replies
973
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
950
views
DECIPHER Package on dada2 -Implementing Silva_metaxa2 training set from qza file into a fastq.gz/.Rdata
DECIPHER dada2
3.1 years ago anrongloh • 0
0
votes
2
replies
821
views
Microbiome 16S amplicon analysis in dada2
bioinformatics DADA2
20 months ago anasjamshed1994 • 0
0
votes
1
reply
767
views
FDR Correction
dada2 Metagenomics DESeq2
updated 2.9 years ago by 41k • written 2.9 years ago by • 0
0
votes
0
replies
761
views
Construct a phyloseq object directly from the dada2 outputs
phyloseq dada2
2.7 years ago Manijeh • 0
2
votes
2
replies
428
views
Broken UNITE 9.0 link (General FASTA Release)
dada2 UNITE
8 months ago GlycineMax • 0
0
votes
0
replies
330
views
Using DADA2 for finding viral sequence variants
VariantDetection dada2 RNASeq
6 months ago Sara • 0
0
votes
0
replies
327
views
is Dada2 biased toward a particular sequence ?
virology dada2 amplican Sequencing RNASeq
6 months ago Sara • 0
22 results • Page 1 of 1
Recent ...
Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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