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BigWig
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0
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1
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2.5k
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bigwig to counts
DESeq2
edgeR
bigwig
limma
3.3 years ago • updated 3.0 years ago
Bogdan
▴ 670
0
votes
2
replies
2.9k
views
converting bedgraph into bigwig
bedgraph
wiggleplotr
bigwig
wig
updated 3.4 years ago by
complaintguide
• 0 • written 3.4 years ago by
Bogdan
▴ 670
0
votes
1
reply
2.1k
views
'Negative' and 'Positive' bigWig RNAseq files: how to deal with these???
bigWig
RNASeqData
4.0 years ago • updated 3.9 years ago
bas_work
▴ 30
0
votes
5
replies
2.8k
views
rtracklayer::import() BigWig issue on windows (solved)
software error
BigWig
import
windows
5.8 years ago
lsilva.m
• 0
0
votes
1
reply
2.8k
views
Plotting bigwig coverage over chromosomal coordinates with wiggleplotr
wiggleplotr
bigwig
coverage
ngs
updated 8.3 years ago by
kaur.alasoo
▴ 30 • written 8.3 years ago by
borgmichael
• 0
3
votes
15
replies
4.3k
views
(Big)wig file of complete chromosome
bigwig
rtracklayer
import
granges
grangeslist
updated 8.5 years ago by
Michael Lawrence
★ 11k • written 8.5 years ago by
Assa Yeroslaviz
★ 1.5k
2
votes
1
reply
1.6k
views
Strange first_time object in rtracklayer import
rtracklayer
bigwig
import
updated 9.2 years ago by
Michael Lawrence
★ 11k • written 9.2 years ago by
zx8754
▴ 10
2
votes
3
replies
1.9k
views
rtracklayer - export.bw bug
bigwig
rtracklayer
export.bw
updated 9.2 years ago by
Michael Lawrence
★ 11k • written 9.2 years ago by
story.benjamin
▴ 20
3
votes
9
replies
3.2k
views
export.bw produces enormous files (10^5 times bigger than they should be)
rtracklayer
bigwig
updated 10.0 years ago by
laurent.lacroix
▴ 30 • written 10.0 years ago by
koneill
▴ 30
0
votes
2
replies
1.6k
views
Rtracklayer creating large temp files when importing BigWigs
rtracklayer
BigWig
updated 10.2 years ago by
Michael Lawrence
★ 11k • written 10.2 years ago by
dborgesrmit
• 0
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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 …
Answer: limpa analysis advice
by
Gordon Smyth
53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
Answer: When to use edgeR or limma
by
Gordon Smyth
53k
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…
Votes
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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