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guideseq
•
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0
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replies
227
views
Error in bam loading in getUniqueCleavageEvents() in GUIDEseq package
GUIDEseq
3 months ago
StayM
• 0
0
votes
6
replies
1.2k
views
Option to override removal of duplicate reads - GUIDEseq
GUIDEseq
updated 2.2 years ago by
Julie Zhu
★ 4.3k • written 2.2 years ago by
sharvari gujja
▴ 40
0
votes
1
reply
696
views
GUIDEseq - Error combining individual steps into the pipeline
GUIDEseq
updated 2.4 years ago by
Julie Zhu
★ 4.3k • written 2.4 years ago by
sharvari gujja
▴ 40
0
votes
0
replies
446
views
GUIDEseq - filtering offtarget sites present in background controls
GUIDEseq
2.4 years ago
sharvari gujja
▴ 40
0
votes
0
replies
486
views
GUIDEseq: read count for each offtarget
GUIDEseq
2.4 years ago
sharvari gujja
▴ 40
0
votes
0
replies
585
views
Question about input to binReads.sh in GUIDEseq
GUIDEseq
2.4 years ago
sharvari gujja
▴ 40
3
votes
1
reply
767
views
Major on-target peak not appearing in GUIDEseq results
GUIDEseq
updated 3.7 years ago by
Julie Zhu
★ 4.3k • written 3.7 years ago by
David Kuo
• 0
0
votes
2
replies
1.0k
views
getUniqueCleavageEvents() not working in GUIDEseq package
GUIDEseq
updated 3.7 years ago by
Julie Zhu
★ 4.3k • written 3.7 years ago by
Tiffany
• 0
0
votes
4
replies
1.1k
views
GUIDEseq Error using offTargetAnalysisOfPeakRegions
GUIDEseq
updated 4.9 years ago by
Julie Zhu
★ 4.3k • written 4.9 years ago by
tomas.rodriguez
▴ 10
1
vote
3
replies
990
views
GUIDEseq BED input error
GUIDEseq
4.9 years ago
tomas.rodriguez
▴ 10
0
votes
2
replies
1.0k
views
GUIDEseq Error in GAlignmentPairs
GAlignmentPairs
GUIDEseq
updated 5.1 years ago by
Julie Zhu
★ 4.3k • written 5.2 years ago by
tomas.rodriguez
▴ 10
0
votes
1
reply
784
views
GUIDEseq outputDir error
GUIDEseq
updated 5.2 years ago by
Julie Zhu
★ 4.3k • written 5.2 years ago by
tomas.rodriguez
▴ 10
0
votes
3
replies
1.1k
views
GUIDEseq plus/minus strand inputs
GUIDEseq
updated 5.2 years ago by
Julie Zhu
★ 4.3k • written 5.2 years ago by
tomas.rodriguez
▴ 10
0
votes
1
reply
745
views
GUIDEseq bam input
GUIDEseq
bam
updated 5.2 years ago by
Julie Zhu
★ 4.3k • written 5.2 years ago by
tomas.rodriguez
▴ 10
0
votes
0
replies
1.1k
views
Analyzing CIRCLE-seq data using GUIDEseq package
GUIDEseq
CIRCLE-seq
7.0 years ago
Julie Zhu
★ 4.3k
2
votes
4
replies
1.7k
views
GUIDESeq analysis - handling biological and technical replicates
guideseq
updated 7.1 years ago by
Julie Zhu
★ 4.3k • written 7.1 years ago by
aamir.mir
• 0
2
votes
1
reply
1.3k
views
createBarcodeFasta in GUIDEseq
GUIDEseq
updated 7.1 years ago by
Julie Zhu
★ 4.3k • written 7.1 years ago by
aamir.mir
• 0
17 results • Page
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Comment: Mostly increased counts in differentially accessible peaks using DESeq2
by
ATpoint
★ 4.5k
Keep in mind that if you add replication then you should do it for all conditions so you can meaningfully regress the inevitable batch effe…
Answer: Automatically generate contrasts from a model matrix / formula
by
Gordon Smyth
51k
I am very concerned that you are attempting to extract pairwise comparisons from an interaction formula like `0 + Group*Sex + Age`, because…
Comment: Mostly increased counts in differentially accessible peaks using DESeq2
by
Ricardo Iván
• 0
Hi Michael, Thanks for your reply. After reviewing the PCAs, maybe the issue that despite the replicates looking similar, there is still a…
Comment: Using Normalized Counts in DESeq2
by
Michael Love
42k
Also, just to add, there are many dozens of posts on this topic of DESeq2 applied to TCGA counts, normalized or other. Recommend google sea…
Answer: Using Normalized Counts in DESeq2
by
ATpoint
★ 4.5k
TCGA raw counts can be obtained for example using the TCGAbiolinks or recount packages.
Votes
Answer: When running contrasts, does it use normalized read counts?
Comment: featureCounts fails to load annotation file
Answer: How to reverse complement some elements of a DNAStringSet
Answer: KEGGgraph result difference
Answer: What should be the normalization protocol for RNA seq data for WGCNA?
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