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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
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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
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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
1.4k
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
643
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
1 of 1
Recent ...
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Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Comment: Too many significant genes when integrating gtex and tcga
by
Michael Love
41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Answer: Too many significant genes when integrating gtex and tcga
by
James W. MacDonald
65k
See `?results`, in particular the lfcThreshold argument.
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
You already ran a temporal assay. Now you can compare each time point to the baseline. The interaction term is only applicable if you have…
Comment: Timecourse RNASeq analysis
by
Aurora
• 0
I managed to run ImpulseDE2 as I am interested in getting significant gene changes over time. Now I would like to run deseq as well and com…
Votes
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
stuck on unimplemented type 'list' in 'EncodeElement'
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