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locatevariants
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4
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8
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2.9k
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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
2.6 years ago
davidhillis
• 0
0
votes
1
reply
905
views
Information about locateVariants function
genomiclocation
canonicaltranscripts
locateVariants
updated 4.1 years ago by
James W. MacDonald
68k • written 4.1 years ago by
Paola
• 0
2
votes
2
replies
1.9k
views
[VariantAnnotation] Preserve query metadata with locateVariants()
variantannotation
locatevariants
metadata
mcols
updated 7.8 years ago by
Valerie Obenchain
★ 6.8k • written 7.9 years ago by
enricoferrero
▴ 680
0
votes
1
reply
1.5k
views
predictCoding errors with: sequence ^1$ not found
variantannotation
predict coding
locateVariants
granges
8.0 years ago
tony j
• 0
0
votes
2
replies
2.0k
views
locateVariants function does not find an annotation for the locus
locatevariants
txdb.hsapiens.ucsc.hg19.knowngene
variantannotation
8.2 years ago
Aleksandra
• 0
0
votes
2
replies
1.9k
views
SNPs in multiple locations
txdb.hsapiens.ucsc.hg19.knowngene
ucsc
annotation
locatevariants
variantannotation
updated 8.3 years ago by
Valerie Obenchain
★ 6.8k • written 8.3 years ago by
Lna
• 0
1
vote
23
replies
3.7k
views
Distance calculation for variants in intergenic regions
locatevariants
variantannotation
genomicfeatures
updated 8.9 years ago by
Michael Lawrence
★ 11k • written 8.9 years ago by
Lna
• 0
1
vote
4
replies
2.6k
views
variantAnnotation::locateVariants() with AllVariants(): why do some input variants not get annotated?
variantannotation
locatevariants
10.2 years ago • updated 10.1 years ago
Jakob Goldmann
• 0
8 results • Page
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Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Did you use the development version as Aaron suggested? There is an argument to read the market matrix file directly into an `SVT_SparseMat…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
dan.gatti
• 0
Was anyone else able to put the pieces together using the reply above? I read in one 10X sample using DropletUtils::read10xCounts() and thi…
Comment: Announcing GBCC 2025: The first-ever joint conference between Bioconductor and G
by
dzv20413
• 0
Wow, GBCC 2025 sounds amazing, can not wait to see the logo contest results! Also, I just played [Level Devil][1] and it is super addictive…
Comment: Memory error while running alignments
by
Erik Wright
▴ 150
How much memory is available on the computer? A distance matrix of 50k sequences requires at least 50k*50k/2 * 8 bytes = 10GB, assuming the…
Comment: NA values for DESeq2 p-values and adjusted p-values using large sample sizes
by
Gabriel
• 0
Thank you very much for the reply. However, none of these three options seems to fit: 1) The genes for which NA appears do not have all 0 …
Votes
Comment: Check removeBatchEffect effectiveness
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
Answer: DESeq2 design for haplotype MPRA
A: Different logFC (log2foldchange) values for genes from limma-voom and other too
Comment: Check removeBatchEffect effectiveness
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