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GenomicRange
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Need Help w/ Subset on GRangesList
GenomicRange
GenomicRanges
3 months ago • updated 12 weeks ago
mat149
▴ 70
0
votes
1
reply
739
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DeSeq2 and GenomicRange installation possible conflict with bioconductor version 3.16?
DESeq2
version3.16
installation
bioconductor
GenomicRange
updated 16 months ago by
James W. MacDonald
65k • written 16 months ago by
hong
• 0
1
vote
11
replies
912
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Finding genes with loss of Heterozygosity
genomicrange
updated 4.0 years ago by
Kevin Blighe
★ 3.9k • written 4.0 years ago by
AZ
▴ 30
5
votes
2
replies
554
views
Intersecting two big dataframe
genomicrange
intersect
updated 4.1 years ago by
James W. MacDonald
65k • written 4.1 years ago by
AZ
▴ 30
4 results • Page
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Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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