Showing : variantannotation • reset
0
votes
2
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122
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VariantAnnotation::readVcf not reading variants
VariantAnnotation
updated 4 weeks ago by 57k • written 5 weeks ago by • 0
0
votes
2
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204
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VCF File too large for tabix. Best option to make it usable with R?
samtools tabix VariantAnnotation VCFArray
updated 11 weeks ago by 6.5k • written 3 months ago by • 0
1
vote
12
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303
views
readVcf does not recognize tabix index
VariantAnnotation readvcf tabix
updated 11 weeks ago by 6.5k • written 3 months ago by • 0
0
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2
replies
108
views
readVCF requires the argument "genome". What does it stand for?
Genome readVcf VariantAnnotation
3 months ago naive • 0
1
vote
1
reply
132
views
Matching Variants Between Two VCF Objects
VariantAnnotation
updated 6 months ago by ▴ 90 • written 7 months ago by ★ 1.5k
2
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2
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162
views
Obtaining Comments From VCF Header
VariantAnnotation VCFHeader
updated 11 months ago by 25k • written 11 months ago by ★ 1.5k
3
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2
replies
168
views
Import or Subset VCF PASS Variants
VariantAnnotation subset ScanVcfParam
updated 14 months ago by 25k • written 14 months ago by ★ 1.5k
0
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2
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133
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Extract structural variant and flanking sequence from VCF and fasta, in R
VariantAnnotation Bioconductor VCF Structural variants R
updated 14 months ago by 25k • written 14 months ago by • 0
0
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1
reply
90
views
Can strand be set to minus in VRanges objects?
VariantAnnotation
updated 17 months ago by 57k • written 17 months ago by • 0
0
votes
1
reply
234
views
FilterVCF Filter '' failed: shape of 'skeleton' is not compatible with 'NROW(flesh)'
variantAnnotation
updated 20 months ago by 25k • written 20 months ago by • 0
2
votes
3
replies
391
views
"Packages required but not available." rtracklayer in OSX is not available to CRAN, resulting in errors for downstream dependencies.
GenomicRanges rtracklayer VariantAnnotation S4Vectors SummarizedExperiment
updated 23 months ago by 13k • written 23 months ago by ▴ 30
2
votes
3
replies
196
views
VariantAnnotation - subset multi-allele variants
variantAnnotation
updated 23 months ago by 11k • written 23 months ago by • 0
0
votes
1
reply
201
views
negative AD value interfering with readVcfasVRanges
VariantAnnotation
updated 2.0 years ago by 11k • written 2.0 years ago by • 0
0
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3
replies
293
views
rbind VCF Two Objects Column Names Error
VariantAnnotation VCF
2.1 years ago Dario Strbenac ★ 1.5k
0
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0
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246
views
predictCoding warning message: serious or not?
software error annotation VariantAnnotation
updated 2.2 years ago by 2.7k • written 2.2 years ago by • 0
2
votes
3
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369
views
Error in VCF parsing with VariantAnnotation
software error VariantAnnotation ensemblVEP
updated 2.3 years ago by ★ 6.7k • written 2.3 years ago by ▴ 20
3
votes
8
replies
452
views
Create protein sequences including variants from a VCF file
VariantAnnotation customProDB
2.3 years ago daniel.magnus.bader ▴ 40
0
votes
1
reply
345
views
VariantAnnotation fails to load VCF record
variantannotation
2.5 years ago Daniel Cameron ▴ 20
0
votes
6
replies
441
views
How to prepare .vcf for seqCAT
seqCAT variantannotation gatk
updated 2.6 years ago by ▴ 30 • written 2.6 years ago by • 0
0
votes
1
reply
295
views
writeVcf save invalid vcf with metadata out of order
variantannotation
updated 2.6 years ago by ★ 6.7k • written 2.6 years ago by ▴ 20
1
vote
7
replies
929
views
Data from ##SAMPLE lines in VCF?
variantannotation coldata
updated 2.7 years ago by ★ 6.7k • written 2.7 years ago by ▴ 10
3
votes
3
replies
504
views
Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
variantannotation
updated 3.0 years ago by ★ 6.7k • written 3.0 years ago by ▴ 10
3
votes
4
replies
509
views
Problem when transforming Platypus vcf to VRanges
variantannotation vcf readvcf vranges
updated 3.0 years ago by 11k • written 3.0 years ago by • 0
0
votes
2
replies
457
views
Error: invalid class "VRanges" object
variantannotation VRanges R Rle
updated 3.0 years ago by ★ 6.7k • written 3.0 years ago by • 0
0
votes
2
replies
508
views
VariantAnnotation::locateVariants error coming from XVector
variantannotation xvector iranges
3.1 years ago Vivek.b ▴ 100
0
votes
2
replies
440
views
filtering a VCF file based on genotype
variantannotation
updated 3.1 years ago by ★ 6.7k • written 3.1 years ago by ▴ 610
0
votes
1
reply
429
views
VariantAnnotation and filtering a VCF
variantannotation
3.1 years ago Bogdan ▴ 610
0
votes
1
reply
436
views
Annotating outdated SNP identifiers
variants variantannotation SNPlocs.Hsapiens.dbSNP150.GRCh38 biomaRt
3.3 years ago sandmann.t ▴ 70
2
votes
2
replies
551
views
[VariantAnnotation] Preserve query metadata with locateVariants()
variantannotation locatevariants metadata mcols
updated 3.5 years ago by ★ 6.7k • written 3.5 years ago by ▴ 570
0
votes
2
replies
2.0k
views
Problem using biocLite() to update packages
biocLite BiocInstaller variantannotation
updated 3.6 years ago by 57k • written 3.6 years ago by ★ 2.0k
0
votes
1
reply
588
views
predictCoding errors with: sequence ^1$ not found
variantannotation predict coding locateVariants granges
3.7 years ago tony j • 0
7
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4
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1.1k
views
BiocGenerics built with R 3.4.2 changes behaviour
biocgenerics iranges variantannotation
updated 3.7 years ago by 15k • written 3.7 years ago by ▴ 40
7
votes
6
replies
860
views
SNP location annotation problem in "VariantAnnotation" package
annotation variantannotation
updated 3.8 years ago by ★ 6.7k • written 3.8 years ago by ▴ 20
0
votes
4
replies
764
views
Translation Error in predictCoding() for VariantAnnotation
VariantAnnotation
updated 3.8 years ago by 15k • written 3.8 years ago by • 0
8
votes
6
replies
970
views
Error when running "locateVariants" function in "VariantAnnotation" package
variantannotation tidyverse genomicfeatures
updated 3.8 years ago by 15k • written 3.8 years ago by ▴ 20
0
votes
2
replies
804
views
locateVariants function does not find an annotation for the locus
locatevariants txdb.hsapiens.ucsc.hg19.knowngene variantannotation
3.9 years ago • updated 3.8 years ago Aleksandra • 0
0
votes
1
reply
839
views
Troubleshooting a histogram DataTrack in Gviz
VariantAnnotation gviz
3.9 years ago Russ Fraser ▴ 10
2
votes
5
replies
1.5k
views
VariantAnnotation: Error with ScanVcfParam
variantannotation vcf readvcf filtervcf scanvcfparam
3.9 years ago Didi ▴ 10
0
votes
2
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616
views
SNPs in multiple locations
txdb.hsapiens.ucsc.hg19.knowngene ucsc annotation locatevariants variantannotation
updated 4.0 years ago by ★ 6.7k • written 4.0 years ago by • 0
0
votes
1
reply
463
views
summarizeVariants from VariantAnnotation reordering genes in rownames
variantannotation summarizevariants
updated 4.0 years ago by ★ 6.7k • written 4.0 years ago by • 0
3
votes
4
replies
664
views
No annotation for single SNPs
variantannotation SNPs txdb.hsapiens.ucsc.hg19.knowngene ucsc
updated 4.0 years ago by ★ 6.7k • written 4.0 years ago by • 0
0
votes
6
replies
1.1k
views
Error using readVcf
gwastools variantannotation
updated 4.0 years ago by ▴ 800 • written 4.0 years ago by • 0
3
votes
3
replies
1.3k
views
VariantAnnotation Installation Failure
VariantAnnotation
updated 4.1 years ago by ★ 6.7k • written 4.1 years ago by ▴ 340
1
vote
2
replies
487
views
Exclude Mutations from Mutation List
variantannotation
updated 4.1 years ago by 25k • written 4.1 years ago by ▴ 110
2
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6
replies
1.1k
views
extracting Allele Read Counts - part2
rsamtools variantannotation
updated 4.2 years ago by 57k • written 4.2 years ago by ▴ 610
0
votes
3
replies
730
views
Error in c(DataFrameList(META = meta), tbls[unique(tags)])
VariantAnnotation
updated 4.2 years ago by 15k • written 4.2 years ago by • 0
1
vote
3
replies
1.2k
views
annotation of SV (Structural Variants)
variantannotation annotationhub
4.2 years ago Bogdan ▴ 610
3
votes
2
replies
770
views
filtering VCF files
variantannotation variantfiltering
updated 4.3 years ago by 11k • written 4.3 years ago by ▴ 610
0
votes
0
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607
views
VariantAnnotation mapToTranscripts: best implementation
VariantAnnotation mapToTranscripts
4.3 years ago kristina_holton • 0
0
votes
2
replies
579
views
does readVcf mistakenly ignore ploidy for missing genotypes?
readvcf gt missing VariantAnnotation
4.3 years ago TimothéeFlutre ▴ 70
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Hey @kevin , Thanks for the helpful posts! I noticed in your link to this heatmap analysis, you used scale() and not vst(). However, in yo…
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Dear Gordon, Thank you so much for your reply. It worked well! I just changed y to t because the protein values were included in dat in my…
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Answer: How does the empirical Bayes moderation (eBayes) in the limma pipeline work?
Differential expression across gene features
C: DESeq on transcripts v/s genes
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DESeq on transcripts v/s genes
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