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paired analysis
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1.0k
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adapter trimming paired vs unpaired reads
rna seq
trimmomatic
trimming
adapter trimming
paired analysis
3.3 years ago
Mozart
▴ 20
2
votes
4
replies
677
views
What's the best way to use "semi" technical replicates with biological replicates?
limma
technical replicates
biological replicates
paired analysis
updated 3.4 years ago by
Aaron Lun
★ 27k • written 3.4 years ago by
paul.alto
▴ 50
0
votes
0
replies
370
views
Paired DE analysis in edgeR with trios of samples while blocking for various confounders
edger
rnaseq
paired analysis
design matrix
3.4 years ago
svlachavas
▴ 800
0
votes
2
replies
341
views
Comparing groups with paired samples by using limma
limma
paired analysis
updated 3.5 years ago by
Gordon Smyth
46k • written 3.5 years ago by
annadv77
• 0
1
vote
8
replies
595
views
Unexpected differences in results from paired analysis with DESeq2
DESEq2
paired analysis
factor levels
updated 4.3 years ago by
Michael Love
37k • written 4.3 years ago by
luisa.bresadola
• 0
5 results • Page
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Answer: Design and contrast matrices for analyzing the effect of two factors of interest
by
Gordon Smyth
46k
> In a typical regression, I would just add them to the model when estimating my coefficients of interest Why not do the same with limma? …
Comment: TPM normalization starting with read counts
by
Gordon Smyth
46k
> So you think my method in TPM normalization that I introduced above is not good? Your computation of RPKM using edgeR is fine, provided …
Comment: error in package GenVisR while installing
by
堃
• 0
Package ‘FField’ was removed from the CRAN repository.[enter link description here][1] I installed FField by using remotes::install_github…
Comment: DESeq 2 failes to load
by
Ruggero
• 0
This solved the error, in case someone else is having compilation errors from installing RSQllite: install.packages('RSQLite', repos='http…
Comment: pathview says my nonmodel species is unknown: "species invalid"
by
Guido Hooiveld
★ 3.3k
A while ago a faced the same for another non-model organism. I was able to get it working using a 'hack'. This hack is nothing more than m…
Votes
DiffBind affinity vs occupancy Heatmaps
Answer: How to remove dendrogram from pheatmaps?
A: conceptual question about FDR, FDR adjusted p-value and q-value
A: conceptual question about FDR, FDR adjusted p-value and q-value
A: How to select summit size for histone ChiP-Seq in Diffbind
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