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ENCODE
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reset
2
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6
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2.5k
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ChIPseeker: covplot function: error with some ENCODE data sets
chiPseeker
covplot
ENCODE
ChIpseq
9.0 years ago
sarabusquets88
• 0
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
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
0
votes
1
reply
421
views
ENCODExplorer metadata Questions
annotation
software error
ENCODE
updated 4.5 years ago by
shepherl
3.9k • written 4.5 years ago by
zhiyue.zhao
• 0
5 results • Page
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Answer: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
> When I search camera limma on pubmed, I found 2 papers I am unclear what point you are trying to make. limma's camera method has been fo…
Comment: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
limma most certainly is available. It installs in R 4.4.0 and Bioc 3.19 for all platforms without any issues. It has not had any period of …
Comment: package goseq seems to be not available on the latest version of R
by
Patrycja
▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
Check the number of bootstrapped data per chromosome compared to the original, and then you can also look at its distribution. For this it'…
Comment: DNAString: Standard checksum function?
by
Henrik Bengtsson
★ 2.4k
For completeness: SEGUID v2 (https://www.seguid.org/), implemented in CRAN package **[seguid](https://cran.r-project.org/package=seguid)*…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
package goseq seems to be not available on the latest version of R
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