Showing : variantannotation • reset
0
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VariantAnnotation::locateVariants error coming from XVector
variantannotation xvector iranges
7.5 years ago Vivek.b ▴ 100
0
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2
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2.4k
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filtering a VCF file based on genotype
variantannotation
updated 7.5 years ago by ★ 6.8k • written 7.5 years ago by ▴ 670
0
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1
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1.8k
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VariantAnnotation and filtering a VCF
variantannotation
7.5 years ago Bogdan ▴ 670
0
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1
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1.6k
views
Annotating outdated SNP identifiers
variants variantannotation SNPlocs.Hsapiens.dbSNP150.GRCh38 biomaRt
7.7 years ago sandmann.t ▴ 70
2
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2
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2.0k
views
[VariantAnnotation] Preserve query metadata with locateVariants()
variantannotation locatevariants metadata mcols
updated 7.9 years ago by ★ 6.8k • written 7.9 years ago by ▴ 680
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2
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3.4k
views
Problem using biocLite() to update packages
biocLite BiocInstaller variantannotation
updated 8.0 years ago by 68k • written 8.0 years ago by ★ 2.0k
0
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1
reply
1.5k
views
predictCoding errors with: sequence ^1$ not found
variantannotation predict coding locateVariants granges
8.1 years ago tony j • 0
7
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4
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2.8k
views
BiocGenerics built with R 3.4.2 changes behaviour
biocgenerics iranges variantannotation
updated 8.1 years ago by 16k • written 8.1 years ago by ▴ 40
7
votes
6
replies
2.4k
views
SNP location annotation problem in "VariantAnnotation" package
annotation variantannotation
updated 8.2 years ago by ★ 6.8k • written 8.2 years ago by ▴ 20
0
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4
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1.9k
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Translation Error in predictCoding() for VariantAnnotation
VariantAnnotation
updated 8.2 years ago by 16k • written 8.2 years ago by • 0
8
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6
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2.6k
views
Error when running "locateVariants" function in "VariantAnnotation" package
variantannotation tidyverse genomicfeatures
updated 8.2 years ago by 16k • written 8.2 years ago by ▴ 20
0
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2
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2.0k
views
locateVariants function does not find an annotation for the locus
locatevariants txdb.hsapiens.ucsc.hg19.knowngene variantannotation
8.3 years ago • updated 8.2 years ago Aleksandra • 0
0
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1
reply
1.8k
views
Troubleshooting a histogram DataTrack in Gviz
VariantAnnotation gviz
8.3 years ago Russ Fraser ▴ 40
2
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5
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3.4k
views
VariantAnnotation: Error with ScanVcfParam
variantannotation vcf readvcf filtervcf scanvcfparam
8.3 years ago Didi ▴ 10
0
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2
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2.0k
views
SNPs in multiple locations
txdb.hsapiens.ucsc.hg19.knowngene ucsc annotation locatevariants variantannotation
updated 8.4 years ago by ★ 6.8k • written 8.4 years ago by • 0
0
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1
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1.1k
views
summarizeVariants from VariantAnnotation reordering genes in rownames
variantannotation summarizevariants
updated 8.4 years ago by ★ 6.8k • written 8.4 years ago by • 0
3
votes
4
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2.0k
views
No annotation for single SNPs
variantannotation SNPs txdb.hsapiens.ucsc.hg19.knowngene ucsc
updated 8.4 years ago by ★ 6.8k • written 8.4 years ago by • 0
0
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6
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3.1k
views
Error using readVcf
gwastools variantannotation
updated 8.4 years ago by ▴ 890 • written 8.4 years ago by • 0
3
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3
replies
3.0k
views
VariantAnnotation Installation Failure
VariantAnnotation
updated 8.5 years ago by ★ 6.8k • written 8.5 years ago by ▴ 370
1
vote
2
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1.2k
views
Exclude Mutations from Mutation List
variantannotation
updated 8.5 years ago by 25k • written 8.5 years ago by ▴ 110
2
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6
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3.4k
views
extracting Allele Read Counts - part2
rsamtools variantannotation
updated 8.6 years ago by 68k • written 8.6 years ago by ▴ 670
0
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3
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1.5k
views
Error in c(DataFrameList(META = meta), tbls[unique(tags)])
VariantAnnotation
updated 8.6 years ago by 16k • written 8.6 years ago by • 0
1
vote
3
replies
2.5k
views
annotation of SV (Structural Variants)
variantannotation annotationhub
8.6 years ago Bogdan ▴ 670
3
votes
2
replies
1.9k
views
filtering VCF files
variantannotation variantfiltering
updated 8.7 years ago by ★ 11k • written 8.7 years ago by ▴ 670
0
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0
replies
1.3k
views
VariantAnnotation mapToTranscripts: best implementation
VariantAnnotation mapToTranscripts
8.7 years ago kristina_holton • 0
0
votes
2
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1.4k
views
does readVcf mistakenly ignore ploidy for missing genotypes?
readvcf gt missing VariantAnnotation
8.7 years ago TimothéeFlutre ▴ 80
2
votes
7
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2.6k
views
VariantAnnotation - expand not working as intended for VCF
variantannotation
updated 8.8 years ago by ★ 11k • written 8.8 years ago by • 0
2
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4
replies
2.7k
views
Best way to create a VRanges object from a large VCF file?
variantannotation readvcf readvcfasvranges vcf
updated 8.8 years ago by ★ 11k • written 8.8 years ago by • 0
3
votes
3
replies
1.8k
views
CollapsedVCF and ExpandedVCF rownames and vcfs with large ref/alt columns
variantannotation VCF
updated 8.9 years ago by ★ 6.8k • written 8.9 years ago by 21k
0
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2
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1.8k
views
Problem with VariantAnnotation and VCF "R" genotype fields when expanding CollapsedVCF
VariantAnnotation bug
updated 9.0 years ago by ★ 6.8k • written 9.0 years ago by 21k
1
vote
3
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1.8k
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VariantAnnotation error with readVcf after genotypeToSnpMatrix
variantannotation
9.0 years ago sarah.williams1 ▴ 40
0
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0
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1.5k
views
Job: PhD Position in Bioinformatics
bioinformatics protein variantannotation data integration Job
9.0 years ago stephan.pabinger • 0
0
votes
1
reply
1.3k
views
VariantAnnotation -filterVcf/FilterRules - 3 fxns as list to FilterRules throughs and erro
filtervcf variantannotation
updated 9.0 years ago by 25k • written 9.0 years ago by ▴ 60
1
vote
23
replies
3.7k
views
Distance calculation for variants in intergenic regions
locatevariants variantannotation genomicfeatures
updated 9.0 years ago by ★ 11k • written 9.0 years ago by • 0
0
votes
7
replies
1.7k
views
VariantAnnotation - filterVcf - Prints multiple vcf headers
variantannotation
updated 9.0 years ago by 25k • written 9.0 years ago by ▴ 60
0
votes
23
replies
3.7k
views
VariantAnnotation geno function
variantannotation
9.0 years ago ribioinfo ▴ 100
3
votes
9
replies
4.1k
views
Annotate VCFs with Cosmic (ExAC etc.) fields
variantannotation cosmic exac
updated 9.0 years ago by 25k • written 9.0 years ago by ▴ 130
0
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2
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1.5k
views
Create VRanges object from mutation data (txt extracted from annotated vcf)
iranges variantannotation
updated 9.1 years ago by ★ 11k • written 9.1 years ago by • 0
2
votes
3
replies
2.0k
views
predictCoding fails with error
VariantAnnotation
9.1 years ago Stephane Plaisance | VIB | ▴ 60
1
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2
replies
1.3k
views
VariantAnnotation CollapsedVCF trouble
variantannotation subsetting
9.1 years ago Fabian Grammes ▴ 20
0
votes
1
reply
1.4k
views
SNP Injection in Custom BSGenome
variantannotation bsgenome
updated 9.2 years ago by 16k • written 9.2 years ago by • 0
1
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2
replies
1.5k
views
Locating enhancers that are mutated
snv granges genomicranges variantannotation indel
updated 9.2 years ago by ★ 11k • written 9.2 years ago by • 0
0
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0
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1.1k
views
After mapping one Sanger sequence read (about 900bp) to hg19 using blastn, How can I get variants presented as reference-based position and base ch…
Biostrings blast variantannotation
9.3 years ago li lilingdu ▴ 450
1
vote
9
replies
1.8k
views
Problem with summarizeVariants function (VariantAnnotation) when using a multi-sample vcf
variantannotation
updated 9.3 years ago by ★ 6.8k • written 9.3 years ago by • 0
0
votes
1
reply
1.2k
views
VariantAnnotation print malformated vcf
variantannotation writevcf
updated 9.3 years ago by ★ 6.8k • written 9.3 years ago by • 0
5
votes
2
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1.7k
views
info(header(vcf)) remembers fields not imported: bugfix?
VariantAnnotation
9.3 years ago kevin.rue ▴ 350
2
votes
2
replies
1.7k
views
readVCFAsVRanges in VariantAnnotation broken by an FTZ format?
variantannotation readvcfasvranges vcf
updated 9.3 years ago by ★ 11k • written 9.3 years ago by ▴ 120
4
votes
10
replies
4.0k
views
Best way to import from multiple VCF files?
variantannotation
updated 9.3 years ago by 4.2k • written 9.3 years ago by ▴ 150
1
vote
2
replies
1.6k
views
Expand annotation on a vcf file
vcf variantannotation
updated 9.4 years ago by ★ 11k • written 9.4 years ago by • 0
3
votes
8
replies
2.6k
views
Vcf to VRanges conversion error: ["incorrect number of dimensions"]
variantannotation somaticsignatures
updated 9.4 years ago by ★ 11k • written 9.4 years ago by • 0
217 results • Page 2 of 5
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Comment: Getting a large intercept with DESeq2 by Michael Love 43k
Thanks James -- Denise you can check the "note on factor levels" in the vignette. And I'd recommend `plotCounts()` for looking at individu…
Comment: Getting a large intercept with DESeq2 by James W. MacDonald 68k
As a trivial example, consider this: ``` > model.matrix(~Treatment, data.frame(Treatment = factor(rep(1:3, each = 4)))) (Intercept) Tre…
Answer: Getting a large intercept with DESeq2 by James W. MacDonald 68k
The default parameterization in R is a treatment-contrasts parameterization that sets one of your groups as the baseline. So the intercept …
Answer: Must I do pseudobulk analysis on Cell Surface Protein Labeling data of Single C by ATpoint ★ 5.0k
There is no "MUST", but pseudobulk aggregation is beneficial to a) enable use of tested and robust methods such as limma (though it could u…
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Yes, we use limpa for PTMs ourselves. I assume your data is preprocessed so that each row corresponds to a PTM. You replace dpcQuant() with…
Votes
Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Using edgeR or DESeq2 to analyze allele-specific expression?
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
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