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locatevariants
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locateVariants function does not find an annotation for the locus
locatevariants
txdb.hsapiens.ucsc.hg19.knowngene
variantannotation
6.7 years ago
Aleksandra
• 0
1
vote
23
replies
2.4k
views
Distance calculation for variants in intergenic regions
locatevariants
variantannotation
genomicfeatures
updated 7.5 years ago by
Michael Lawrence
★ 11k • written 7.5 years ago by
Lna
• 0
0
votes
2
replies
1.4k
views
SNPs in multiple locations
txdb.hsapiens.ucsc.hg19.knowngene
ucsc
annotation
locatevariants
variantannotation
updated 6.8 years ago by
Valerie Obenchain
★ 6.8k • written 6.8 years ago by
Lna
• 0
1
vote
4
replies
2.2k
views
variantAnnotation::locateVariants() with AllVariants(): why do some input variants not get annotated?
variantannotation
locatevariants
8.7 years ago
Jakob Goldmann
• 0
4
votes
8
replies
1.5k
views
TxDB.Hsapiens.UCSC.hg38.knownGene with locateVariants() identifying SNPs from various chromosome being part of the same gene
MetID
TxDB.Hsapiens.UCSC.hg38.knownGene
locateVariants
GenomicFeatures
VariantAnnotation
13 months ago
davidhillis
• 0
2
votes
2
replies
1.4k
views
[VariantAnnotation] Preserve query metadata with locateVariants()
variantannotation
locatevariants
metadata
mcols
updated 6.4 years ago by
Valerie Obenchain
★ 6.8k • written 6.4 years ago by
enricoferrero
▴ 660
0
votes
1
reply
644
views
Information about locateVariants function
genomiclocation
canonicaltranscripts
locateVariants
updated 2.6 years ago by
James W. MacDonald
65k • written 2.6 years ago by
Paola
• 0
0
votes
1
reply
1.2k
views
predictCoding errors with: sequence ^1$ not found
variantannotation
predict coding
locateVariants
granges
6.5 years ago
tony j
• 0
8 results • Page
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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…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
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
A: Print Differentially Expressed Exons From Dexseq Results
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