Showing : VariantAnnotation • reset
0
votes
0
replies
69
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
7 days ago Stevie Pederson • 0
0
votes
1
reply
132
views
Is random access by row index possible for an indexed VCF file?
Rsamtools VariantAnnotation
updated 5 weeks ago by 65k • written 5 weeks ago by ▴ 170
0
votes
0
replies
148
views
RFC: significant changes to ensemblVEP package
VariantAnnotation ensemblVEP
3 months ago Vincent J. Carey, Jr. 6.7k
0
votes
5
replies
459
views
locateVariant from VariantAnnotation returns wrong results
VariantAnnotation locateVariant
updated 4 months ago by 65k • written 4 months ago by ▴ 30
0
votes
0
replies
429
views
Variant Filtering on very large VCF files
VariantAnnotation VariantFiltering
6 months ago Bogdan ▴ 670
2
votes
2
replies
1.4k
views
Matching Variants Between Two VCF Objects
VariantAnnotation
written 3.4 years ago by ★ 1.5k
0
votes
2
replies
526
views
Docker usage with Trio Bioconductor Package
VariantAnnotation docker trio
updated 11 months ago by ★ 4.0k • written 11 months ago by • 0
4
votes
8
replies
1.4k
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
13 months ago davidhillis • 0
0
votes
0
replies
459
views
VariantAnnotation::readVcf incorrectly processes GATK Mutect2 vcf INFO field AS_SB_TABLE
vcf AS_SB_TABLE readVcf Mutect2 VariantAnnotation
14 months ago therealgenna • 0
0
votes
3
replies
993
views
Add GP values to VCF
VariantAnnotation
15 months ago Stephanie M. Gogarten ▴ 870
0
votes
1
reply
1.4k
views
Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123 VariantFiltering Alignment VariantAnnotation
updated 17 months ago by 65k • written 17 months ago by ▴ 30
2
votes
4
replies
925
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
19 months ago rwan.work • 0
0
votes
2
replies
726
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
19 months ago rwan.work • 0
0
votes
2
replies
2.6k
views
merging VCF files
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
written 11.3 years ago by ▴ 870
0
votes
3
replies
992
views
Problem with intronic variants in VariantAnnotation
VariantAnnotation
updated 2.1 years ago by • 0 • written 2.3 years ago by • 0
0
votes
2
replies
1.0k
views
Reading vcf file with readVcf
VariantAnnotation
2.6 years ago aurelien.dejode • 0
0
votes
2
replies
800
views
Multiple exons for predictCoding() from VariantAnnotation (use phase information from gff3 file)?
VariantAnnotation
updated 2.6 years ago by 16k • written 2.8 years ago by • 0
0
votes
5
replies
1.3k
views
installation error: Error in setIs(class2, cli, extensionObject = obji, doComplete = FALSE and setClass() for chromVAR and VariantAnnotation
Install VariantAnnotation Bioconductor chromVAR
updated 2.7 years ago by 6.7k • written 2.7 years ago by • 0
0
votes
1
reply
867
views
GRanges object out-of-bound
VariantAnnotation
updated 2.6 years ago by 6.7k • written 2.7 years ago by • 0
2
votes
3
replies
1.0k
views
readVcf(remoteFile, "hg19", "region") works on macos, fails on linux and in docker
open.BcfFile VariantAnnotation
updated 3 months ago by • 0 • written 2.8 years ago by ▴ 470
0
votes
0
replies
589
views
Annotate mutations on DNA level to splice transcripts
VariantAnnotation
2.8 years ago Kasper_holm2 • 0
0
votes
4
replies
1.5k
views
Error of read in large vcf file using readVcf
SomaticSignatures VariantAnnotation
updated 2.8 years ago by 65k • written 2.8 years ago by • 0
0
votes
2
replies
1.2k
views
VariantAnnotation::readVcf not reading variants
VariantAnnotation
updated 2.9 years ago by 65k • written 2.9 years ago by • 0
0
votes
2
replies
2.2k
views
VCF File too large for tabix. Best option to make it usable with R?
samtools tabix VariantAnnotation VCFArray
updated 3.0 years ago by 6.7k • written 3.1 years ago by • 0
1
vote
12
replies
2.9k
views
readVcf does not recognize tabix index
VariantAnnotation readvcf tabix
updated 3.0 years ago by 6.7k • written 3.1 years ago by • 0
0
votes
2
replies
1.2k
views
readVCF requires the argument "genome". What does it stand for?
Genome readVcf VariantAnnotation
3.1 years ago naive • 0
2
votes
2
replies
1.2k
views
Obtaining Comments From VCF Header
VariantAnnotation VCFHeader
updated 3.8 years ago by 25k • written 3.8 years ago by ★ 1.5k
3
votes
2
replies
1.3k
views
Import or Subset VCF PASS Variants
VariantAnnotation subset ScanVcfParam
updated 4.0 years ago by 25k • written 4.0 years ago by ★ 1.5k
0
votes
2
replies
1.1k
views
Extract structural variant and flanking sequence from VCF and fasta, in R
VariantAnnotation Bioconductor VCF Structural variants R
updated 4.0 years ago by 25k • written 4.0 years ago by • 0
0
votes
1
reply
644
views
Can strand be set to minus in VRanges objects?
VariantAnnotation
updated 4.3 years ago by 65k • written 4.3 years ago by • 0
0
votes
1
reply
1.2k
views
FilterVCF Filter '' failed: shape of 'skeleton' is not compatible with 'NROW(flesh)'
variantAnnotation
updated 4.5 years ago by 25k • written 4.5 years ago by • 0
2
votes
3
replies
1.5k
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 4.8 years ago by ★ 13k • written 4.8 years ago by ▴ 30
2
votes
3
replies
926
views
VariantAnnotation - subset multi-allele variants
variantAnnotation
updated 4.8 years ago by ★ 11k • written 4.8 years ago by • 0
0
votes
1
reply
759
views
negative AD value interfering with readVcfasVRanges
VariantAnnotation
updated 4.8 years ago by ★ 11k • written 4.9 years ago by • 0
0
votes
3
replies
1.0k
views
rbind VCF Two Objects Column Names Error
VariantAnnotation VCF
4.9 years ago Dario Strbenac ★ 1.5k
0
votes
0
replies
758
views
predictCoding warning message: serious or not?
software error annotation VariantAnnotation
updated 5.1 years ago by 3.8k • written 5.1 years ago by • 0
2
votes
3
replies
1.4k
views
Error in VCF parsing with VariantAnnotation
software error VariantAnnotation ensemblVEP
updated 5.1 years ago by ★ 6.8k • written 5.1 years ago by ▴ 20
3
votes
8
replies
3.0k
views
Create protein sequences including variants from a VCF file
VariantAnnotation customProDB
5.1 years ago daniel.magnus.bader ▴ 40
0
votes
1
reply
926
views
VariantAnnotation fails to load VCF record
variantannotation
5.4 years ago Daniel Cameron ▴ 40
0
votes
6
replies
1.5k
views
How to prepare .vcf for seqCAT
seqCAT variantannotation gatk
updated 5.4 years ago by ▴ 30 • written 5.4 years ago by • 0
0
votes
1
reply
821
views
writeVcf save invalid vcf with metadata out of order
variantannotation
updated 5.4 years ago by ★ 6.8k • written 5.4 years ago by ▴ 20
1
vote
7
replies
3.1k
views
Data from ##SAMPLE lines in VCF?
variantannotation coldata
updated 5.6 years ago by ★ 6.8k • written 5.6 years ago by ▴ 10
3
votes
3
replies
1.3k
views
Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
variantannotation
updated 5.8 years ago by ★ 6.8k • written 5.8 years ago by ▴ 10
3
votes
4
replies
1.7k
views
Problem when transforming Platypus vcf to VRanges
variantannotation vcf readvcf vranges
updated 5.8 years ago by ★ 11k • written 5.8 years ago by • 0
0
votes
2
replies
1.2k
views
Error: invalid class "VRanges" object
variantannotation VRanges R Rle
updated 5.8 years ago by ★ 6.8k • written 5.8 years ago by • 0
0
votes
2
replies
1.2k
views
VariantAnnotation::locateVariants error coming from XVector
variantannotation xvector iranges
5.9 years ago Vivek.b ▴ 100
0
votes
2
replies
1.5k
views
filtering a VCF file based on genotype
variantannotation
updated 5.9 years ago by ★ 6.8k • written 5.9 years ago by ▴ 670
0
votes
1
reply
1.1k
views
VariantAnnotation and filtering a VCF
variantannotation
6.0 years ago Bogdan ▴ 670
0
votes
1
reply
1.1k
views
Annotating outdated SNP identifiers
variants variantannotation SNPlocs.Hsapiens.dbSNP150.GRCh38 biomaRt
6.1 years ago sandmann.t ▴ 70
2
votes
2
replies
1.4k
views
[VariantAnnotation] Preserve query metadata with locateVariants()
variantannotation locatevariants metadata mcols
updated 6.3 years ago by ★ 6.8k • written 6.3 years ago by ▴ 660
50 results • Page 1 of 1
Recent ...
Replies
Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) …
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param by russ.bainer ▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Chris • 0
Hi Robert, If I don't want to use all pathway in c2 gene set but only a few pathways of interested, how can I do that? So we try to get a …
Comment: How to retrieve detailed regression results from deseq2 by Weiqian ▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Awards • All
Popular Question to James W. MacDonald 65k
Popular Question to shepherl 3.8k
Popular Question to BioinfGuru ▴ 30
Popular Question to Gordon Smyth 50k
Scholar to Peter Hickey ▴ 740
Locations • All
France, just now
WEHI, Melbourne, Australia, 5 minutes ago
Ghana/KNUST, 5 minutes ago
EMBL Heidelberg, 19 minutes ago
Heidelberg, 27 minutes ago
Traffic: 604 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6