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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
23 months ago
davidhillis
• 0
0
votes
1
reply
805
views
Information about locateVariants function
genomiclocation
canonicaltranscripts
locateVariants
updated 3.4 years ago by
James W. MacDonald
68k • written 3.4 years ago by
Paola
• 0
2
votes
2
replies
1.7k
views
[VariantAnnotation] Preserve query metadata with locateVariants()
variantannotation
locatevariants
metadata
mcols
updated 7.2 years ago by
Valerie Obenchain
★ 6.8k • written 7.2 years ago by
enricoferrero
▴ 680
0
votes
1
reply
1.3k
views
predictCoding errors with: sequence ^1$ not found
variantannotation
predict coding
locateVariants
granges
7.3 years ago
tony j
• 0
0
votes
2
replies
1.8k
views
locateVariants function does not find an annotation for the locus
locatevariants
txdb.hsapiens.ucsc.hg19.knowngene
variantannotation
7.5 years ago
Aleksandra
• 0
0
votes
2
replies
1.7k
views
SNPs in multiple locations
txdb.hsapiens.ucsc.hg19.knowngene
ucsc
annotation
locatevariants
variantannotation
updated 7.6 years ago by
Valerie Obenchain
★ 6.8k • written 7.6 years ago by
Lna
• 0
1
vote
23
replies
2.9k
views
Distance calculation for variants in intergenic regions
locatevariants
variantannotation
genomicfeatures
updated 8.3 years ago by
Michael Lawrence
★ 11k • written 8.3 years ago by
Lna
• 0
1
vote
4
replies
2.5k
views
variantAnnotation::locateVariants() with AllVariants(): why do some input variants not get annotated?
variantannotation
locatevariants
9.5 years ago
Jakob Goldmann
• 0
8 results • Page
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Comment: How to formulate 2 factor nested design in DESeq2
by
Mariane
• 0
Hi JK Kim, I'm having a problem similar to the one you reported. Could you please tell me how you solved this problem? Thanks
Comment: batch effect removal for agilent microarray data
by
gaye.yilmaz
• 0
Thank you
Answer: Pathview visualisation not including positive log2 fold changes
by
James W. MacDonald
68k
Without providing a self-contained example, nobody can tell you if/where you went wrong. Since you get a KEGG pathway with some of the gene…
Comment: Differential variance analysis - can i use deseq2
by
Marwan
• 0
Thanks Michael for your answer, i didnt mean to use Deseq2 directly for the variance testing, but more like asking if using the (VST) data…
Answer: Differential variance analysis - can i use deseq2
by
Michael Love
43k
We don't have a test of differential variance but other Bioconductor packages can, check similar posts (even on the right side bar) or use …
Votes
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Suggesting changing the "reply-to" field to the mailing list address.
Answer: UniProt.ws query for single UniRef90 ID takes several minutes
A: How to extract DESeq2 results for an interaction design
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
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