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ENCODE
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2
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ChIPseeker: covplot function: error with some ENCODE data sets
chiPseeker
covplot
ENCODE
ChIpseq
9.0 years ago
sarabusquets88
• 0
0
votes
2
replies
1.5k
views
How to take sample peak from each chromosome in peak bed files ?
r
chipseq
encode
peak
7.4 years ago
Jurat Shahidin
▴ 80
3
votes
3
replies
1.4k
views
Broken AnnotationHub resource (AH25517 | wgEncodeOpenChromDnaseGm12878Pk.narrowPeak.gz)
annotationhub
encode
updated 8.1 years ago by
Valerie Obenchain
★ 6.8k • written 8.1 years ago by
Peter Hickey
▴ 740
5
votes
2
replies
1.2k
views
AnnotationHub: two broad peaks from same url are not the same
annotationhub
bugs
encode
bed
7.4 years ago
wcstcyx
▴ 30
0
votes
1
reply
415
views
ENCODExplorer metadata Questions
annotation
software error
ENCODE
updated 4.5 years ago by
shepherl
3.8k • written 4.5 years ago by
zhiyue.zhao
• 0
5 results • Page
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Comment: More regions in union when increasing DBA$config$mergeOverlap
by
Ian D.
▴ 70
Hello. Thanks for the reply. Sorry about this. My testing is telling me that 1 is the default (a gap), not -1 (1bp overlap). Negative …
Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★ 4.1k
> I am just re-processing due to being uncertain about how they used the edgeR analysis to reach gene level edgeR devs published something…
Comment: Differences in differential analysis methods for RNA-Seq
by
james.zhang20
• 0
Thanks for the explanations, it has helped clarify some things. Unfortunately, I am working from an early access public dataset (https://do…
Answer: Deseq2 and Normalization of RNA sequencing data
by
ATpoint
★ 4.1k
There is no expectation of normality that is realistic in terms of expression level. Levels are widely different between genes, and counts …
Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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