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locatevariants
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4
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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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Replies
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
That's weird. Using the example data works for me. ``` > example(read10xCounts) rd10xC> # Mocking up some 10X genomics output. rd10xC> ex…
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teamardigen
• 0
Sounds like an exciting event for anyone passionate about small molecule innovation. The focus on discovery and optimization really drives …
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
dan.gatti
• 0
I am, but perhaps I'm not understanding how it should work. > sse = DropletUtils::read10xCounts(curr_files[1], mtx.class = 'SVT_Sparse…
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…
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Drug datasets for RNA-seq
Comment: Check removeBatchEffect effectiveness
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
Answer: DESeq2 design for haplotype MPRA
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