Showing : variantannotation • reset
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merging VCF files
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
written 9.6 years ago by ▴ 820
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3
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389
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Problem with intronic variants in VariantAnnotation
VariantAnnotation
updated 5 months ago by • 0 • written 7 months ago by • 0
0
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2
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307
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Reading vcf file with readVcf
VariantAnnotation
10 months ago aurelien.dejode • 0
0
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2
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321
views
Multiple exons for predictCoding() from VariantAnnotation (use phase information from gff3 file)?
VariantAnnotation
updated 11 months ago by 15k • written 13 months ago by • 0
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5
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519
views
installation error: Error in setIs(class2, cli, extensionObject = obji, doComplete = FALSE and setClass() for chromVAR and VariantAnnotation
Install VariantAnnotation Bioconductor chromVAR
updated 11 months ago by 6.6k • written 12 months ago by • 0
0
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1
reply
274
views
GRanges object out-of-bound
VariantAnnotation
updated 11 months ago by 6.6k • written 12 months ago by • 0
2
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3
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437
views
readVcf(remoteFile, "hg19", "region") works on macos, fails on linux and in docker
open.BcfFile VariantAnnotation
updated 8 months ago by • 0 • written 13 months ago by ▴ 470
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0
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222
views
Annotate mutations on DNA level to splice transcripts
VariantAnnotation
13 months ago Kasper_holm2 • 0
0
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4
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418
views
Error of read in large vcf file using readVcf
SomaticSignatures VariantAnnotation
updated 13 months ago by 60k • written 13 months ago by • 0
0
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2
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426
views
VariantAnnotation::readVcf not reading variants
VariantAnnotation
updated 15 months ago by 60k • written 15 months ago by • 0
0
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2
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834
views
VCF File too large for tabix. Best option to make it usable with R?
samtools tabix VariantAnnotation VCFArray
updated 16 months ago by 6.6k • written 17 months ago by • 0
1
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12
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1.1k
views
readVcf does not recognize tabix index
VariantAnnotation readvcf tabix
updated 16 months ago by 6.6k • written 17 months ago by • 0
0
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2
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339
views
readVCF requires the argument "genome". What does it stand for?
Genome readVcf VariantAnnotation
17 months ago naive • 0
1
vote
1
reply
497
views
Matching Variants Between Two VCF Objects
VariantAnnotation
updated 20 months ago by ▴ 90 • written 20 months ago by ★ 1.5k
2
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2
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376
views
Obtaining Comments From VCF Header
VariantAnnotation VCFHeader
updated 2.1 years ago by 25k • written 2.1 years ago by ★ 1.5k
3
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2
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508
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Import or Subset VCF PASS Variants
VariantAnnotation subset ScanVcfParam
updated 2.3 years ago by 25k • written 2.3 years ago by ★ 1.5k
0
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2
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408
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Extract structural variant and flanking sequence from VCF and fasta, in R
VariantAnnotation Bioconductor VCF Structural variants R
updated 2.4 years ago by 25k • written 2.4 years ago by • 0
0
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1
reply
249
views
Can strand be set to minus in VRanges objects?
VariantAnnotation
updated 2.6 years ago by 60k • written 2.6 years ago by • 0
0
votes
1
reply
464
views
FilterVCF Filter '' failed: shape of 'skeleton' is not compatible with 'NROW(flesh)'
variantAnnotation
updated 2.9 years ago by 25k • written 2.9 years ago by • 0
2
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3
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753
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 3.1 years ago by 13k • written 3.1 years ago by ▴ 30
2
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3
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355
views
VariantAnnotation - subset multi-allele variants
variantAnnotation
updated 3.1 years ago by 11k • written 3.1 years ago by • 0
0
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1
reply
360
views
negative AD value interfering with readVcfasVRanges
VariantAnnotation
updated 3.2 years ago by 11k • written 3.2 years ago by • 0
0
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3
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505
views
rbind VCF Two Objects Column Names Error
VariantAnnotation VCF
3.2 years ago Dario Strbenac ★ 1.5k
0
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0
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404
views
predictCoding warning message: serious or not?
software error annotation VariantAnnotation
updated 3.4 years ago by 3.2k • written 3.4 years ago by • 0
2
votes
3
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711
views
Error in VCF parsing with VariantAnnotation
software error VariantAnnotation ensemblVEP
updated 3.4 years ago by ★ 6.7k • written 3.4 years ago by ▴ 20
3
votes
8
replies
1.2k
views
Create protein sequences including variants from a VCF file
VariantAnnotation customProDB
3.5 years ago • updated 3.4 years ago daniel.magnus.bader ▴ 40
0
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1
reply
527
views
VariantAnnotation fails to load VCF record
variantannotation
3.7 years ago Daniel Cameron ▴ 40
0
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6
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848
views
How to prepare .vcf for seqCAT
seqCAT variantannotation gatk
updated 3.7 years ago by ▴ 30 • written 3.7 years ago by • 0
0
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1
reply
440
views
writeVcf save invalid vcf with metadata out of order
variantannotation
updated 3.7 years ago by ★ 6.7k • written 3.8 years ago by ▴ 20
1
vote
7
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1.7k
views
Data from ##SAMPLE lines in VCF?
variantannotation coldata
updated 3.9 years ago by ★ 6.7k • written 3.9 years ago by ▴ 10
3
votes
3
replies
673
views
Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
variantannotation
updated 4.1 years ago by ★ 6.7k • written 4.1 years ago by ▴ 10
3
votes
4
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912
views
Problem when transforming Platypus vcf to VRanges
variantannotation vcf readvcf vranges
updated 4.1 years ago by 11k • written 4.1 years ago by • 0
0
votes
2
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643
views
Error: invalid class "VRanges" object
variantannotation VRanges R Rle
updated 4.1 years ago by ★ 6.7k • written 4.1 years ago by • 0
0
votes
2
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712
views
VariantAnnotation::locateVariants error coming from XVector
variantannotation xvector iranges
4.2 years ago Vivek.b ▴ 100
0
votes
2
replies
705
views
filtering a VCF file based on genotype
variantannotation
updated 4.2 years ago by ★ 6.7k • written 4.3 years ago by ▴ 640
0
votes
1
reply
595
views
VariantAnnotation and filtering a VCF
variantannotation
4.3 years ago Bogdan ▴ 640
0
votes
1
reply
596
views
Annotating outdated SNP identifiers
variants variantannotation SNPlocs.Hsapiens.dbSNP150.GRCh38 biomaRt
4.4 years ago sandmann.t ▴ 70
2
votes
2
replies
763
views
[VariantAnnotation] Preserve query metadata with locateVariants()
variantannotation locatevariants metadata mcols
updated 4.7 years ago by ★ 6.7k • written 4.7 years ago by ▴ 620
0
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2
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2.3k
views
Problem using biocLite() to update packages
biocLite BiocInstaller variantannotation
updated 4.8 years ago by 60k • written 4.8 years ago by ★ 2.0k
0
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1
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755
views
predictCoding errors with: sequence ^1$ not found
variantannotation predict coding locateVariants granges
4.8 years ago tony j • 0
7
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4
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1.4k
views
BiocGenerics built with R 3.4.2 changes behaviour
biocgenerics iranges variantannotation
updated 4.9 years ago by 15k • written 4.9 years ago by ▴ 40
7
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6
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1.1k
views
SNP location annotation problem in "VariantAnnotation" package
annotation variantannotation
updated 4.9 years ago by ★ 6.7k • written 5.0 years ago by ▴ 20
0
votes
4
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1.0k
views
Translation Error in predictCoding() for VariantAnnotation
VariantAnnotation
updated 4.9 years ago by 15k • written 5.0 years ago by • 0
8
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6
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1.4k
views
Error when running "locateVariants" function in "VariantAnnotation" package
variantannotation tidyverse genomicfeatures
updated 4.9 years ago by 15k • written 5.0 years ago by ▴ 20
0
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2
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997
views
locateVariants function does not find an annotation for the locus
locatevariants txdb.hsapiens.ucsc.hg19.knowngene variantannotation
5.0 years ago Aleksandra • 0
0
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1
reply
1.0k
views
Troubleshooting a histogram DataTrack in Gviz
VariantAnnotation gviz
5.0 years ago Russ Fraser ▴ 20
2
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5
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1.8k
views
VariantAnnotation: Error with ScanVcfParam
variantannotation vcf readvcf filtervcf scanvcfparam
5.0 years ago Didi ▴ 10
0
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2
replies
821
views
SNPs in multiple locations
txdb.hsapiens.ucsc.hg19.knowngene ucsc annotation locatevariants variantannotation
updated 5.1 years ago by ★ 6.7k • written 5.1 years ago by • 0
0
votes
1
reply
592
views
summarizeVariants from VariantAnnotation reordering genes in rownames
variantannotation summarizevariants
updated 5.1 years ago by ★ 6.7k • written 5.2 years ago by • 0
3
votes
4
replies
913
views
No annotation for single SNPs
variantannotation SNPs txdb.hsapiens.ucsc.hg19.knowngene ucsc
updated 5.2 years ago by ★ 6.7k • written 5.2 years ago by • 0
50 results • Page 1 of 1
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Comment: How should I set my eps value in cluster profiler? by Guido Hooiveld ★ 3.3k
Under the hood `clusterProfiler` makes use of a (fast) GSEA algorithm implemented in the package `fgsea` (function `fgseaMultilevel`). The …
Comment: Error using ChAMP SVD analysis by CristEin • 0
In fact, I found that the author may have caused the problem class(myNorm) %>% length() #equals 2 class(myNorm) == "data.…
Comment: Error in Create switchAnalyzeRlist by k.vitting.seerup ▴ 120
Oh sorry I missed the species. Yes they also match for chicken :-) (both being called "ENSGALT..."). The other is from NCBI
Comment: Error in Create switchAnalyzeRlist by bpshtiwan ▴ 10
Ok, have you looked cDNA fasta file for Chicken (maternal Broiler) Gallus gallus? I am using Kallisto for alignment and quantification. He…
Comment: DEXseq error unable to find an inherited method for function NSBS for signature by ta_awwad ▴ 10
Hi there, did you manage to solve this problem? thanks TA
Votes
DEXseq error unable to find an inherited method for function NSBS for signature CompressedIntegerList
Answer: Error in Create switchAnalyzeRlist
Answer: Error in Create switchAnalyzeRlist
A: DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Ge
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
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