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plyranges
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2
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3
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1.7k
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Combine GRanges(List) to a single GRanges with unified breakpoints
GenomicRanges
plyranges
21 months ago
Rodrigo
• 0
1
vote
1
reply
688
views
plyranges select() when a metadata column is shared with core variable
plyranges
2.4 years ago • updated 2.2 years ago
Michael Love
41k
0
votes
0
replies
701
views
Using genomicRanges / plyranges to calculate score of peaks within intervals
plyranges
GenomicRanges
3.0 years ago
alorsonmethyle
• 0
0
votes
0
replies
1.2k
views
Reducing and aggregating GRanges with gaps using plyranges
GenomicRanges
plyranges
3.5 years ago
r.a.policastro
• 0
3
votes
12
replies
2.0k
views
Understanding group_by, reduce_ranges,
plyranges
granges
updated 4.4 years ago by
lee.s
▴ 70 • written 4.4 years ago by
Konstantinos Yeles
▴ 80
1
vote
5
replies
1.7k
views
Annotating GRanges with TxDb gene models using plyranges
plyranges
4.5 years ago
Aditya
▴ 160
4
votes
8
replies
1.5k
views
the closest gene to a breakpoint
granges
plyranges
updated 5.6 years ago by
Gordon Smyth
50k • written 5.6 years ago by
Bogdan
▴ 670
7 results • Page
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Comment: Input Question for deseq.r
by
ATpoint
★ 4.0k
It is unclear what "deseq.r" is. It is not part of DESeq2, and almost certainly no part of RSeqAn. Please add details, and keep in mind tha…
Answer: DESEQ2 output gives multiple groups when only 2 groups are present
by
ATpoint
★ 4.0k
In the first PCA plot there is almost certainly some hidden character like whitespaces in the column from colData that encodes this group. …
Answer: A ComBat-seq issue: the covariates are confounded
by
ATpoint
★ 4.0k
```r > table(batch, group) group batch egfr gfp her2 1 0 12 5 2 6 6 0 ``` All of her2 is batch2, all of egfr i…
Comment: DESeq2 setting significant p-value
by
Dev
• 0
after running DESeq2 does it sort the value on the basis of pvalue, or anything, or does it give the data back in the input format I have …
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
But wouldn't this result in a different gene set for each analysis stratification? How can you then compare if maybe gene x comes up in Tim…
Votes
Comment: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
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