Showing : variantannotation • reset
0
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183
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VariantAnnotation not does escape = within header string quotes
VariantAnnotation
updated 9 weeks ago by ★ 4.0k • written 9 weeks ago by ▴ 40
0
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1
reply
423
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Problem using locateVariants() from the VariantAnnotation package
VariantAnnotation vari
10 months ago Marco • 0
0
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1
reply
679
views
ensemblVEP deprecation and how to reproduce
VariantAnnotation
updated 16 months ago by 6.7k • written 16 months ago by • 0
0
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0
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711
views
Using variantAnnotation to put together genotype and consequence information
variantAnn VariantAnnotation
18 months ago ramiro.barrantes ▴ 10
1
vote
2
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2.1k
views
How to compare subset of samples from VCF files
VCF VariantAnnotation
updated 19 months ago by 53k • written 19 months ago by • 0
0
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0
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623
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
21 months ago Stevie Pederson • 0
2
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1
reply
779
views
Is random access by row index possible for an indexed VCF file?
Rsamtools VariantAnnotation
updated 22 months ago by 68k • written 22 months ago by ▴ 180
0
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0
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574
views
RFC: significant changes to ensemblVEP package
VariantAnnotation ensemblVEP
2.0 years ago Vincent J. Carey, Jr. 6.7k
0
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5
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1.2k
views
locateVariant from VariantAnnotation returns wrong results
VariantAnnotation locateVariant
updated 2.1 years ago by 68k • written 2.1 years ago by ▴ 70
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0
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1.4k
views
Variant Filtering on very large VCF files
VariantAnnotation VariantFiltering
2.3 years ago Bogdan ▴ 670
2
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2
replies
2.2k
views
Matching Variants Between Two VCF Objects
VariantAnnotation
written 5.1 years ago by ★ 1.6k
0
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2
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1.2k
views
Docker usage with Trio Bioconductor Package
VariantAnnotation docker trio
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
4
votes
8
replies
3.2k
views
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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0
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1.0k
views
VariantAnnotation::readVcf incorrectly processes GATK Mutect2 vcf INFO field AS_SB_TABLE
vcf AS_SB_TABLE readVcf Mutect2 VariantAnnotation
2.9 years ago therealgenna • 0
0
votes
3
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2.1k
views
Add GP values to VCF
VariantAnnotation
3.0 years ago Stephanie M. Gogarten ▴ 890
0
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1
reply
3.2k
views
Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123 VariantFiltering Alignment VariantAnnotation
updated 3.2 years ago by 68k • written 3.2 years ago by ▴ 30
2
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4
replies
1.7k
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
3.3 years ago rwan.work • 0
0
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2
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1.4k
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
3.3 years ago rwan.work • 0
0
votes
2
replies
3.3k
views
merging VCF files
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
written 13.0 years ago by ▴ 890
0
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3
replies
1.7k
views
Problem with intronic variants in VariantAnnotation
VariantAnnotation
updated 3.9 years ago by • 0 • written 4.0 years ago by • 0
0
votes
2
replies
1.9k
views
Reading vcf file with readVcf
VariantAnnotation
4.3 years ago aurelien.dejode • 0
0
votes
2
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1.3k
views
Multiple exons for predictCoding() from VariantAnnotation (use phase information from gff3 file)?
VariantAnnotation
updated 4.4 years ago by 16k • written 4.5 years ago by • 0
0
votes
5
replies
2.2k
views
installation error: Error in setIs(class2, cli, extensionObject = obji, doComplete = FALSE and setClass() for chromVAR and VariantAnnotation
Install VariantAnnotation Bioconductor chromVAR
updated 4.4 years ago by 6.7k • written 4.4 years ago by • 0
0
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1
reply
1.4k
views
GRanges object out-of-bound
VariantAnnotation
updated 4.4 years ago by 6.7k • written 4.5 years ago by • 0
2
votes
3
replies
1.6k
views
readVcf(remoteFile, "hg19", "region") works on macos, fails on linux and in docker
open.BcfFile VariantAnnotation
updated 24 months ago by • 0 • written 4.5 years ago by ▴ 470
0
votes
0
replies
924
views
Annotate mutations on DNA level to splice transcripts
VariantAnnotation
4.5 years ago Kasper_holm2 • 0
0
votes
4
replies
2.7k
views
Error of read in large vcf file using readVcf
SomaticSignatures VariantAnnotation
updated 4.5 years ago by 68k • written 4.5 years ago by • 0
0
votes
2
replies
1.9k
views
VariantAnnotation::readVcf not reading variants
VariantAnnotation
updated 4.7 years ago by 68k • written 4.7 years ago by • 0
0
votes
2
replies
3.6k
views
VCF File too large for tabix. Best option to make it usable with R?
samtools tabix VariantAnnotation VCFArray
updated 4.8 years ago by 6.7k • written 4.9 years ago by • 0
1
vote
12
replies
5.0k
views
readVcf does not recognize tabix index
VariantAnnotation readvcf tabix
updated 4.8 years ago by 6.7k • written 4.8 years ago by • 0
0
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2
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2.2k
views
readVCF requires the argument "genome". What does it stand for?
Genome readVcf VariantAnnotation
4.8 years ago naive • 0
2
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4
replies
2.2k
views
Obtaining Comments From VCF Header
VariantAnnotation VCFHeader
written 5.5 years ago by ★ 1.6k
3
votes
2
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2.0k
views
Import or Subset VCF PASS Variants
VariantAnnotation subset ScanVcfParam
updated 5.7 years ago by 25k • written 5.7 years ago by ★ 1.6k
0
votes
2
replies
1.9k
views
Extract structural variant and flanking sequence from VCF and fasta, in R
VariantAnnotation Bioconductor VCF Structural variants R
updated 5.8 years ago by 25k • written 5.8 years ago by • 0
0
votes
1
reply
1.0k
views
Can strand be set to minus in VRanges objects?
VariantAnnotation
updated 6.0 years ago by 68k • written 6.0 years ago by • 0
0
votes
1
reply
1.8k
views
FilterVCF Filter '' failed: shape of 'skeleton' is not compatible with 'NROW(flesh)'
variantAnnotation
updated 6.3 years ago by 25k • written 6.3 years ago by • 0
2
votes
3
replies
2.3k
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 6.5 years ago by ★ 13k • written 6.5 years ago by ▴ 30
2
votes
3
replies
1.7k
views
VariantAnnotation - subset multi-allele variants
variantAnnotation
updated 6.5 years ago by ★ 11k • written 6.5 years ago by • 0
0
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1
reply
1.2k
views
negative AD value interfering with readVcfasVRanges
VariantAnnotation
updated 6.6 years ago by ★ 11k • written 6.6 years ago by • 0
0
votes
3
replies
1.5k
views
rbind VCF Two Objects Column Names Error
VariantAnnotation VCF
6.6 years ago Dario Strbenac ★ 1.6k
0
votes
0
replies
1.2k
views
predictCoding warning message: serious or not?
software error annotation VariantAnnotation
updated 6.8 years ago by 4.3k • written 6.8 years ago by • 0
2
votes
3
replies
2.2k
views
Error in VCF parsing with VariantAnnotation
software error VariantAnnotation ensemblVEP
updated 6.8 years ago by ★ 6.8k • written 6.8 years ago by ▴ 20
4
votes
9
replies
4.7k
views
Create protein sequences including variants from a VCF file
VariantAnnotation customProDB
updated 20 months ago by • 0 • written 6.9 years ago by ▴ 50
0
votes
1
reply
1.3k
views
VariantAnnotation fails to load VCF record
variantannotation
7.1 years ago Daniel Cameron ▴ 40
0
votes
6
replies
2.3k
views
How to prepare .vcf for seqCAT
seqCAT variantannotation gatk
updated 7.1 years ago by ▴ 30 • written 7.1 years ago by • 0
0
votes
1
reply
1.3k
views
writeVcf save invalid vcf with metadata out of order
variantannotation
updated 7.2 years ago by ★ 6.8k • written 7.2 years ago by ▴ 20
1
vote
7
replies
4.5k
views
Data from ##SAMPLE lines in VCF?
variantannotation coldata
updated 7.3 years ago by ★ 6.8k • written 7.3 years ago by ▴ 10
3
votes
3
replies
1.9k
views
Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
variantannotation
updated 7.5 years ago by ★ 6.8k • written 7.6 years ago by ▴ 10
3
votes
4
replies
2.4k
views
Problem when transforming Platypus vcf to VRanges
variantannotation vcf readvcf vranges
updated 7.5 years ago by ★ 11k • written 7.5 years ago by • 0
0
votes
2
replies
1.7k
views
Error: invalid class "VRanges" object
variantannotation VRanges R Rle
updated 7.6 years ago by ★ 6.8k • written 7.6 years ago by • 0
217 results • Page 1 of 5
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Comment: Question about the filterByExpr function inputs in edgeR by Gordon Smyth 53k
Regarding edgeR v4 filtering, I didn't mention anything about a minimum count of 10 but rather said "a positive count". So a minimalistic f…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by JKim • 0
Hi Emily, He left some comments regarding normalization. Here is the relevant quote: > The EList object produced by dpcQuant(), containi…
Comment: Joining different datasets and analyzing using the group-specific condition effe by James W. MacDonald 68k
Yes, making a group factor simplifies things, and you will need a new column for disease subject to avoid having a design that is not full …
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Yes, Gender is more a nuisance factor in our experiment, and our primary interest is to compare groups. I will just use filter…
Comment: Joining different datasets and analyzing using the group-specific condition effe by jason.chai • 0
Thank you very much. I had read that and wondered if I used the recommendation in DESeq vignette, I would lose the pairing between groups? …
Votes
Answer: Question about the filterByExpr function inputs in edgeR
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
Comment: Clarification on counting in Rsubread (featureCounts)
C: ControlGenes/ housekeeping genes Deseq2
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