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locatevariants
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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
0
votes
1
reply
634
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
2
votes
2
replies
1.4k
views
[VariantAnnotation] Preserve query metadata with locateVariants()
variantannotation
locatevariants
metadata
mcols
updated 6.3 years ago by
Valerie Obenchain
★ 6.8k • written 6.3 years ago by
enricoferrero
▴ 660
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
0
votes
2
replies
1.5k
views
locateVariants function does not find an annotation for the locus
locatevariants
txdb.hsapiens.ucsc.hg19.knowngene
variantannotation
6.7 years ago
Aleksandra
• 0
0
votes
2
replies
1.3k
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
23
replies
2.4k
views
Distance calculation for variants in intergenic regions
locatevariants
variantannotation
genomicfeatures
updated 7.4 years ago by
Michael Lawrence
★ 11k • written 7.4 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
8.6 years ago
Jakob Goldmann
• 0
8 results • Page
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Comment: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures
by
Gordon Smyth
50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma
by
Gordon Smyth
50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups.
by
Chris
• 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with doctor know about Alzheimer and they don't expect significan…
Comment: Single-Cell Data Simulation from Bulk RNA-seq
by
wichaidi
• 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Votes
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.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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