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locatevariants
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4
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8
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1.5k
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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
14 months ago
davidhillis
• 0
0
votes
1
reply
650
views
Information about locateVariants function
genomiclocation
canonicaltranscripts
locateVariants
updated 2.7 years ago by
James W. MacDonald
66k • written 2.7 years ago by
Paola
• 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
1.2k
views
predictCoding errors with: sequence ^1$ not found
variantannotation
predict coding
locateVariants
granges
6.6 years ago
tony j
• 0
0
votes
2
replies
1.6k
views
locateVariants function does not find an annotation for the locus
locatevariants
txdb.hsapiens.ucsc.hg19.knowngene
variantannotation
6.8 years ago
Aleksandra
• 0
0
votes
2
replies
1.4k
views
SNPs in multiple locations
txdb.hsapiens.ucsc.hg19.knowngene
ucsc
annotation
locatevariants
variantannotation
updated 6.9 years ago by
Valerie Obenchain
★ 6.8k • written 6.9 years ago by
Lna
• 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
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
8 results • Page
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Comment: ChAMP installation issue
by
Tahirah
• 0
Hello. Could you please share how you managed to install ChAMP in R 4.4.0? I also have R 4.4.0 and Bioconductor 3.19 version and ChAMP fail…
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
by
James W. MacDonald
66k
Yes, you can use `limma`.
Comment: Ensembl plants at annotationHub?
by
Johannes Rainer
★ 2.0k
You can get the `EnsDb` EnsDb.Taestivum.v112.sqlite (for Ensembl 112/ ensemblgenomes 59) [here](https://www.dropbox.com/sh/msic0luivbldmb7/…
Answer: Errors in chromosome annotation-biomaRt
by
James W. MacDonald
66k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat
by
James W. MacDonald
66k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Votes
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
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