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AllelicImbalance
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5
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7
replies
2.1k
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Allele Specific Expression Using edgeR
edger
allelicimbalance
8.0 years ago
ugwu.nelson
▴ 10
1
vote
1
reply
992
views
Does the AI package also allow more than one seqlevel?
AllelicImbalance
updated 8.5 years ago by
lasfol
▴ 10 • written 8.5 years ago by
sannysandra93
• 0
1
vote
1
reply
967
views
DESeq2 for allele-specific expression with contrasts between conditions
DESeq2
AllelicImbalance
edgeR
RNASeq
updated 2.9 years ago by
Michael Love
41k • written 2.9 years ago by
Katya
• 0
0
votes
2
replies
1.3k
views
Error message from 'scanForHeterozygotes' function in AllelicImbalance package
allelicimbalance
updated 8.9 years ago by
Jesper Robert Gadin
▴ 20 • written 9.2 years ago by
JK
▴ 10
0
votes
4
replies
1.4k
views
AllelicImbalance with VCFs?
RNASeq
Cancer
trio
AllelicImbalance
RNASeq
Cancer
trio
AllelicImbalance
updated 10.3 years ago by
Jesper Robert Gadin
▴ 20 • written 10.3 years ago by
Tim Triche, Jr.
▴ 10
0
votes
2
replies
1.5k
views
Error using 'scanForHeterozygotes' function in AllelicImbalance package
allelicimbalance
updated 8.9 years ago by
Jesper Robert Gadin
▴ 20 • written 9.2 years ago by
JK
▴ 10
0
votes
1
reply
1.1k
views
AlleicImbalance error reading in BAM files
allelicimbalance
updated 9.3 years ago by
Martin Morgan
25k • written 9.3 years ago by
JK
▴ 10
0
votes
2
replies
1.2k
views
AllelicImbalance error with getAlleleCounts
allelicimbalance
getallelecounts
updated 9.3 years ago by
Valerie Obenchain
★ 6.8k • written 9.3 years ago by
JK
▴ 10
8 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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