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GUIDEseq
•
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0
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replies
427
views
Error in bam loading in getUniqueCleavageEvents() in GUIDEseq package
GUIDEseq
17 months ago
StayM
• 0
0
votes
6
replies
1.6k
views
Option to override removal of duplicate reads - GUIDEseq
GUIDEseq
updated 3.4 years ago by
Julie Zhu
★ 4.3k • written 3.4 years ago by
sharvari gujja
▴ 40
0
votes
1
reply
907
views
GUIDEseq - Error combining individual steps into the pipeline
GUIDEseq
updated 3.6 years ago by
Julie Zhu
★ 4.3k • written 3.6 years ago by
sharvari gujja
▴ 40
0
votes
0
replies
661
views
GUIDEseq - filtering offtarget sites present in background controls
GUIDEseq
3.6 years ago
sharvari gujja
▴ 40
0
votes
0
replies
660
views
GUIDEseq: read count for each offtarget
GUIDEseq
3.6 years ago
sharvari gujja
▴ 40
0
votes
0
replies
759
views
Question about input to binReads.sh in GUIDEseq
GUIDEseq
3.6 years ago
sharvari gujja
▴ 40
3
votes
1
reply
1.0k
views
Major on-target peak not appearing in GUIDEseq results
GUIDEseq
updated 4.8 years ago by
Julie Zhu
★ 4.3k • written 4.8 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 6.0 years ago by
Julie Zhu
★ 4.3k • written 6.0 years ago by
tomas.rodriguez
▴ 10
1
vote
3
replies
1.2k
views
GUIDEseq BED input error
GUIDEseq
6.0 years ago
tomas.rodriguez
▴ 10
0
votes
2
replies
1.3k
views
GUIDEseq Error in GAlignmentPairs
GAlignmentPairs
GUIDEseq
updated 6.3 years ago by
Julie Zhu
★ 4.3k • written 6.3 years ago by
tomas.rodriguez
▴ 10
0
votes
1
reply
989
views
GUIDEseq outputDir error
GUIDEseq
updated 6.3 years ago by
Julie Zhu
★ 4.3k • written 6.3 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
948
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
8.1 years ago
Julie Zhu
★ 4.3k
2
votes
4
replies
2.0k
views
GUIDESeq analysis - handling biological and technical replicates
guideseq
updated 8.3 years ago by
Julie Zhu
★ 4.3k • written 8.3 years ago by
aamir.mir
• 0
2
votes
1
reply
1.5k
views
createBarcodeFasta in GUIDEseq
GUIDEseq
updated 8.3 years ago by
Julie Zhu
★ 4.3k • written 8.3 years ago by
aamir.mir
• 0
17 results • Page
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Replies
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
by
Michael Love
43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA
by
Gordon Smyth
53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study
by
ATpoint
★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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