Showing : locateVariants • reset
4
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8
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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
2.8 years ago davidhillis • 0
0
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1
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960
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Information about locateVariants function
genomiclocation canonicaltranscripts locateVariants
updated 4.3 years ago by 68k • written 4.3 years ago by • 0
2
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2
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2.1k
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[VariantAnnotation] Preserve query metadata with locateVariants()
variantannotation locatevariants metadata mcols
updated 8.1 years ago by ★ 6.8k • written 8.1 years ago by ▴ 680
0
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1
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1.5k
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predictCoding errors with: sequence ^1$ not found
variantannotation predict coding locateVariants granges
8.2 years ago tony j • 0
0
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2
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2.1k
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locateVariants function does not find an annotation for the locus
locatevariants txdb.hsapiens.ucsc.hg19.knowngene variantannotation
8.4 years ago Aleksandra • 0
0
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2
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2.1k
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SNPs in multiple locations
txdb.hsapiens.ucsc.hg19.knowngene ucsc annotation locatevariants variantannotation
updated 8.6 years ago by ★ 6.8k • written 8.6 years ago by • 0
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23
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Distance calculation for variants in intergenic regions
locatevariants variantannotation genomicfeatures
updated 9.2 years ago by ★ 11k • written 9.2 years ago by • 0
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4
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variantAnnotation::locateVariants() with AllVariants(): why do some input variants not get annotated?
variantannotation locatevariants
10.4 years ago Jakob Goldmann • 0
8 results • Page 1 of 1
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Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
The short answer is that limpa reads standard feature-level intensities from Spectronaut or other quantifications tools. limpa is designed …
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Noted, thank you very much.
Votes
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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