Showing : variantannotation • reset
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36
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Reading vcf file with readVcf
VariantAnnotation
updated 8 hours ago by 58k • written 14 hours ago by • 0
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2
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167
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Multiple exons for predictCoding() from VariantAnnotation (use phase information from gff3 file)?
VariantAnnotation
updated 26 days ago by 15k • written 9 weeks ago by • 0
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5
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197
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installation error: Error in setIs(class2, cli, extensionObject = obji, doComplete = FALSE and setClass() for chromVAR and VariantAnnotation
Install VariantAnnotation Bioconductor chromVAR
updated 27 days ago by 6.5k • written 5 weeks ago by • 0
0
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1
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86
views
GRanges object out-of-bound
VariantAnnotation
updated 26 days ago by 6.5k • written 8 weeks ago by • 0
2
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3
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226
views
readVcf(remoteFile, "hg19", "region") works on macos, fails on linux and in docker
open.BcfFile VariantAnnotation
updated 9 weeks ago by • 0 • written 10 weeks ago by ▴ 460
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0
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94
views
Annotate mutations on DNA level to splice transcripts
VariantAnnotation
9 weeks ago Kasper_holm2 • 0
0
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4
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150
views
Error of read in large vcf file using readVcf
SomaticSignatures VariantAnnotation
updated 11 weeks ago by 58k • written 11 weeks ago by • 0
0
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2
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201
views
VariantAnnotation::readVcf not reading variants
VariantAnnotation
updated 4 months ago by 58k • written 4 months ago by • 0
0
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2
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323
views
VCF File too large for tabix. Best option to make it usable with R?
samtools tabix VariantAnnotation VCFArray
updated 5 months ago by 6.5k • written 6 months ago by • 0
1
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12
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487
views
readVcf does not recognize tabix index
VariantAnnotation readvcf tabix
updated 5 months ago by 6.5k • written 6 months ago by • 0
0
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2
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157
views
readVCF requires the argument "genome". What does it stand for?
Genome readVcf VariantAnnotation
6 months ago naive • 0
1
vote
1
reply
204
views
Matching Variants Between Two VCF Objects
VariantAnnotation
updated 9 months ago by ▴ 90 • written 10 months ago by ★ 1.5k
2
votes
2
replies
215
views
Obtaining Comments From VCF Header
VariantAnnotation VCFHeader
updated 14 months ago by 25k • written 14 months ago by ★ 1.5k
3
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2
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238
views
Import or Subset VCF PASS Variants
VariantAnnotation subset ScanVcfParam
updated 17 months ago by 25k • written 17 months ago by ★ 1.5k
0
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2
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188
views
Extract structural variant and flanking sequence from VCF and fasta, in R
VariantAnnotation Bioconductor VCF Structural variants R
updated 17 months ago by 25k • written 17 months ago by • 0
0
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1
reply
129
views
Can strand be set to minus in VRanges objects?
VariantAnnotation
updated 20 months ago by 58k • written 20 months ago by • 0
0
votes
1
reply
287
views
FilterVCF Filter '' failed: shape of 'skeleton' is not compatible with 'NROW(flesh)'
variantAnnotation
updated 23 months ago by 25k • written 23 months ago by • 0
2
votes
3
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471
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 2.2 years ago by 13k • written 2.2 years ago by ▴ 30
2
votes
3
replies
245
views
VariantAnnotation - subset multi-allele variants
variantAnnotation
updated 2.2 years ago by 11k • written 2.2 years ago by • 0
0
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1
reply
241
views
negative AD value interfering with readVcfasVRanges
VariantAnnotation
updated 2.3 years ago by 11k • written 2.3 years ago by • 0
0
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3
replies
358
views
rbind VCF Two Objects Column Names Error
VariantAnnotation VCF
2.3 years ago Dario Strbenac ★ 1.5k
0
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0
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288
views
predictCoding warning message: serious or not?
software error annotation VariantAnnotation
updated 2.5 years ago by 2.8k • written 2.5 years ago by • 0
2
votes
3
replies
442
views
Error in VCF parsing with VariantAnnotation
software error VariantAnnotation ensemblVEP
updated 2.5 years ago by ★ 6.7k • written 2.5 years ago by ▴ 20
3
votes
8
replies
585
views
Create protein sequences including variants from a VCF file
VariantAnnotation customProDB
2.6 years ago • updated 2.5 years ago daniel.magnus.bader ▴ 40
0
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1
reply
395
views
VariantAnnotation fails to load VCF record
variantannotation
2.8 years ago Daniel Cameron ▴ 20
0
votes
6
replies
530
views
How to prepare .vcf for seqCAT
seqCAT variantannotation gatk
updated 2.8 years ago by ▴ 30 • written 2.8 years ago by • 0
0
votes
1
reply
338
views
writeVcf save invalid vcf with metadata out of order
variantannotation
updated 2.8 years ago by ★ 6.7k • written 2.8 years ago by ▴ 20
1
vote
7
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1.1k
views
Data from ##SAMPLE lines in VCF?
variantannotation coldata
updated 3.0 years ago by ★ 6.7k • written 3.0 years ago by ▴ 10
3
votes
3
replies
552
views
Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
variantannotation
updated 3.2 years ago by ★ 6.7k • written 3.2 years ago by ▴ 10
3
votes
4
replies
612
views
Problem when transforming Platypus vcf to VRanges
variantannotation vcf readvcf vranges
updated 3.2 years ago by 11k • written 3.2 years ago by • 0
0
votes
2
replies
510
views
Error: invalid class "VRanges" object
variantannotation VRanges R Rle
updated 3.2 years ago by ★ 6.7k • written 3.2 years ago by • 0
0
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2
replies
564
views
VariantAnnotation::locateVariants error coming from XVector
variantannotation xvector iranges
3.3 years ago Vivek.b ▴ 100
0
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2
replies
498
views
filtering a VCF file based on genotype
variantannotation
updated 3.3 years ago by ★ 6.7k • written 3.4 years ago by ▴ 620
0
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1
reply
469
views
VariantAnnotation and filtering a VCF
variantannotation
3.4 years ago Bogdan ▴ 620
0
votes
1
reply
482
views
Annotating outdated SNP identifiers
variants variantannotation SNPlocs.Hsapiens.dbSNP150.GRCh38 biomaRt
3.5 years ago sandmann.t ▴ 70
2
votes
2
replies
624
views
[VariantAnnotation] Preserve query metadata with locateVariants()
variantannotation locatevariants metadata mcols
updated 3.8 years ago by ★ 6.7k • written 3.8 years ago by ▴ 570
0
votes
2
replies
2.1k
views
Problem using biocLite() to update packages
biocLite BiocInstaller variantannotation
updated 3.9 years ago by 58k • written 3.9 years ago by ★ 2.0k
0
votes
1
reply
630
views
predictCoding errors with: sequence ^1$ not found
variantannotation predict coding locateVariants granges
3.9 years ago tony j • 0
7
votes
4
replies
1.2k
views
BiocGenerics built with R 3.4.2 changes behaviour
biocgenerics iranges variantannotation
updated 4.0 years ago by 15k • written 4.0 years ago by ▴ 40
7
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6
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934
views
SNP location annotation problem in "VariantAnnotation" package
annotation variantannotation
updated 4.0 years ago by ★ 6.7k • written 4.1 years ago by ▴ 20
0
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4
replies
822
views
Translation Error in predictCoding() for VariantAnnotation
VariantAnnotation
updated 4.0 years ago by 15k • written 4.1 years ago by • 0
8
votes
6
replies
1.0k
views
Error when running "locateVariants" function in "VariantAnnotation" package
variantannotation tidyverse genomicfeatures
updated 4.0 years ago by 15k • written 4.1 years ago by ▴ 20
0
votes
2
replies
849
views
locateVariants function does not find an annotation for the locus
locatevariants txdb.hsapiens.ucsc.hg19.knowngene variantannotation
4.1 years ago Aleksandra • 0
0
votes
1
reply
895
views
Troubleshooting a histogram DataTrack in Gviz
VariantAnnotation gviz
4.1 years ago Russ Fraser ▴ 20
2
votes
5
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1.6k
views
VariantAnnotation: Error with ScanVcfParam
variantannotation vcf readvcf filtervcf scanvcfparam
4.1 years ago Didi ▴ 10
0
votes
2
replies
659
views
SNPs in multiple locations
txdb.hsapiens.ucsc.hg19.knowngene ucsc annotation locatevariants variantannotation
updated 4.2 years ago by ★ 6.7k • written 4.2 years ago by • 0
0
votes
1
reply
498
views
summarizeVariants from VariantAnnotation reordering genes in rownames
variantannotation summarizevariants
updated 4.2 years ago by ★ 6.7k • written 4.3 years ago by • 0
3
votes
4
replies
726
views
No annotation for single SNPs
variantannotation SNPs txdb.hsapiens.ucsc.hg19.knowngene ucsc
updated 4.2 years ago by ★ 6.7k • written 4.3 years ago by • 0
0
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6
replies
1.2k
views
Error using readVcf
gwastools variantannotation
updated 4.3 years ago by ▴ 800 • written 4.3 years ago by • 0
3
votes
3
replies
1.4k
views
VariantAnnotation Installation Failure
VariantAnnotation
updated 4.3 years ago by ★ 6.7k • written 4.3 years ago by ▴ 340
50 results • Page 1 of 1
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Comment: Returning to edgeR version 3.26.1? by mvanhorn • 0
Thank you very much for your reply! Our project is a reanalysis of large sets of RNA-seq data to identify circular RNAs using the CIRIquan…
Comment: "full model matrix is less than full rank" by ATpoint ▴ 840
My best guess is that young and old are not "young" or "old" but include some hidden whitespaces like " young" or "old ". That would then m…
Answer: Reading vcf file with readVcf by James W. MacDonald 58k
Usually when you run out of RAM, you usually get an error saying that 'R couldn't allocate a vector of size <some number>'. When it just sa…
Answer: Genic annotations of whole hg38 by James W. MacDonald 58k
What exactly do you mean by 'proportion of genic annotations'? One possibility would be to see what proportion of all the exons are covered…
Answer: Understanding output of Negative Binomial in DESeq2 by Michael Love 34k
> Does this mean that there are seven genes in total that will have significant adjusted p-value? yes > i recall when multiple linea…
Votes
Answer: Swish direction of comparison based on order of factors
Comment: Gradient dotplot
Answer: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi
Answer: Effect size using likelihood ratio test in DESeq2
Comment: ggtree install
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