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GUIDEseq
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0
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replies
421
views
Error in bam loading in getUniqueCleavageEvents() in GUIDEseq package
GUIDEseq
16 months ago
StayM
• 0
0
votes
6
replies
1.6k
views
Option to override removal of duplicate reads - GUIDEseq
GUIDEseq
updated 3.3 years ago by
Julie Zhu
★ 4.3k • written 3.3 years ago by
sharvari gujja
▴ 40
0
votes
1
reply
895
views
GUIDEseq - Error combining individual steps into the pipeline
GUIDEseq
updated 3.5 years ago by
Julie Zhu
★ 4.3k • written 3.5 years ago by
sharvari gujja
▴ 40
0
votes
0
replies
657
views
GUIDEseq - filtering offtarget sites present in background controls
GUIDEseq
3.5 years ago
sharvari gujja
▴ 40
0
votes
0
replies
654
views
GUIDEseq: read count for each offtarget
GUIDEseq
3.5 years ago
sharvari gujja
▴ 40
0
votes
0
replies
751
views
Question about input to binReads.sh in GUIDEseq
GUIDEseq
3.5 years ago
sharvari gujja
▴ 40
3
votes
1
reply
1.0k
views
Major on-target peak not appearing in GUIDEseq results
GUIDEseq
updated 4.7 years ago by
Julie Zhu
★ 4.3k • written 4.7 years ago by
David Kuo
• 0
0
votes
2
replies
1.3k
views
getUniqueCleavageEvents() not working in GUIDEseq package
GUIDEseq
updated 4.8 years ago by
Julie Zhu
★ 4.3k • written 4.8 years ago by
Tiffany
• 0
0
votes
4
replies
1.5k
views
GUIDEseq Error using offTargetAnalysisOfPeakRegions
GUIDEseq
updated 5.9 years ago by
Julie Zhu
★ 4.3k • written 5.9 years ago by
tomas.rodriguez
▴ 10
1
vote
3
replies
1.2k
views
GUIDEseq BED input error
GUIDEseq
5.9 years ago
tomas.rodriguez
▴ 10
0
votes
2
replies
1.3k
views
GUIDEseq Error in GAlignmentPairs
GAlignmentPairs
GUIDEseq
updated 6.2 years ago by
Julie Zhu
★ 4.3k • written 6.2 years ago by
tomas.rodriguez
▴ 10
0
votes
1
reply
980
views
GUIDEseq outputDir error
GUIDEseq
updated 6.2 years ago by
Julie Zhu
★ 4.3k • written 6.2 years ago by
tomas.rodriguez
▴ 10
0
votes
3
replies
1.4k
views
GUIDEseq plus/minus strand inputs
GUIDEseq
updated 6.3 years ago by
Julie Zhu
★ 4.3k • written 6.3 years ago by
tomas.rodriguez
▴ 10
0
votes
1
reply
933
views
GUIDEseq bam input
GUIDEseq
bam
updated 6.3 years ago by
Julie Zhu
★ 4.3k • written 6.3 years ago by
tomas.rodriguez
▴ 10
0
votes
0
replies
1.4k
views
Analyzing CIRCLE-seq data using GUIDEseq package
GUIDEseq
CIRCLE-seq
8.0 years ago
Julie Zhu
★ 4.3k
2
votes
4
replies
2.0k
views
GUIDESeq analysis - handling biological and technical replicates
guideseq
updated 8.2 years ago by
Julie Zhu
★ 4.3k • written 8.2 years ago by
aamir.mir
• 0
2
votes
1
reply
1.5k
views
createBarcodeFasta in GUIDEseq
GUIDEseq
updated 8.2 years ago by
Julie Zhu
★ 4.3k • written 8.2 years ago by
aamir.mir
• 0
17 results • Page
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Comment: Getting a large intercept with DESeq2
by
Michael Love
43k
Thanks James -- Denise you can check the "note on factor levels" in the vignette. And I'd recommend `plotCounts()` for looking at individu…
Comment: Getting a large intercept with DESeq2
by
James W. MacDonald
68k
As a trivial example, consider this: ``` > model.matrix(~Treatment, data.frame(Treatment = factor(rep(1:3, each = 4)))) (Intercept) Tre…
Answer: Getting a large intercept with DESeq2
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68k
The default parameterization in R is a treatment-contrasts parameterization that sets one of your groups as the baseline. So the intercept …
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There is no "MUST", but pseudobulk aggregation is beneficial to a) enable use of tested and robust methods such as limma (though it could u…
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53k
Yes, we use limpa for PTMs ourselves. I assume your data is preprocessed so that each row corresponds to a PTM. You replace dpcQuant() with…
Votes
Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Using edgeR or DESeq2 to analyze allele-specific expression?
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
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