Showing : seqnames • reset
0
votes
5
replies
4.6k
views
Grange object subsetting using seqnames
Seqnames makeGRangesFromDataFrame GRanges Subsetting GenomicRanges
4.6 years ago rtrivedi1 ▴ 10
2
votes
1
reply
1.2k
views
DNAStringSet to DNAStringSetList according to pattern in sequence names
dnastringset dnastringsetlist seqnames
7.2 years ago s.ghignone ▴ 10
0
votes
1
reply
1.4k
views
GenomeInfoDb: where are the genome patches?
seqnames genomeinfodb
updated 8.6 years ago by 16k • written 8.7 years ago by ▴ 10
0
votes
2
replies
2.5k
views
GenomicRanges: `seqnames<-` can not work as expected
genomicranges seqnames factor
9.2 years ago wcstcyx ▴ 30
0
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1
reply
1.2k
views
error in noGGi
software error seqnames characters r chipseq
9.7 years ago awakumaya • 0
17
votes
4
replies
19k
views
How to properly sort GRanges?
granges genomicranges sort seqnames order
updated 10.8 years ago by ▴ 30 • written 11.2 years ago by ▴ 680
0
votes
6
replies
7.4k
views
GRanges: problem with multiple seqnames and seqlengths
GRanges seqnames seqlengths IRanges
11.3 years ago topher.hamm • 0
7 results • Page 1 of 1
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Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink by ja569116 • 0
Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
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It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
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The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
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Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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