Showing : variantAnnotation • reset
0
votes
0
replies
89
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
21 days ago Stevie Pederson • 0
0
votes
1
reply
148
views
Is random access by row index possible for an indexed VCF file?
Rsamtools VariantAnnotation
updated 7 weeks ago by 65k • written 7 weeks ago by ▴ 180
0
votes
0
replies
164
views
RFC: significant changes to ensemblVEP package
VariantAnnotation ensemblVEP
3 months ago Vincent J. Carey, Jr. 6.7k
0
votes
5
replies
484
views
locateVariant from VariantAnnotation returns wrong results
VariantAnnotation locateVariant
updated 5 months ago by 65k • written 5 months ago by ▴ 30
0
votes
0
replies
452
views
Variant Filtering on very large VCF files
VariantAnnotation VariantFiltering
7 months ago Bogdan ▴ 670
2
votes
2
replies
1.5k
views
Matching Variants Between Two VCF Objects
VariantAnnotation
written 3.4 years ago by ★ 1.5k
0
votes
2
replies
546
views
Docker usage with Trio Bioconductor Package
VariantAnnotation docker trio
updated 11 months ago by ★ 4.1k • 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
478
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
1.0k
views
Add GP values to VCF
VariantAnnotation
16 months ago • updated 15 months ago Stephanie M. Gogarten ▴ 870
0
votes
1
reply
1.5k
views
Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123 VariantFiltering Alignment VariantAnnotation
updated 18 months ago by 65k • written 18 months ago by ▴ 30
2
votes
4
replies
944
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
19 months ago rwan.work • 0
0
votes
2
replies
748
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
1.0k
views
Problem with intronic variants in VariantAnnotation
VariantAnnotation
updated 2.2 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
812
views
Multiple exons for predictCoding() from VariantAnnotation (use phase information from gff3 file)?
VariantAnnotation
updated 2.7 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
882
views
GRanges object out-of-bound
VariantAnnotation
updated 2.7 years ago by 6.7k • written 2.8 years ago by • 0
2
votes
3
replies
1.1k
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
601
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 3.0 years ago by 65k • written 3.0 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 3.1 years ago by 6.7k • written 3.2 years ago by • 0
1
vote
12
replies
3.0k
views
readVcf does not recognize tabix index
VariantAnnotation readvcf tabix
updated 3.1 years ago by 6.7k • written 3.1 years ago by • 0
0
votes
2
replies
1.3k
views
readVCF requires the argument "genome". What does it stand for?
Genome readVcf VariantAnnotation
3.1 years ago naive • 0
2
votes
2
replies
1.3k
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 4.1 years ago by 25k • written 4.1 years ago by • 0
0
votes
1
reply
657
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 4.6 years ago by 25k • written 4.6 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
946
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
770
views
negative AD value interfering with readVcfasVRanges
VariantAnnotation
updated 4.9 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
773
views
predictCoding warning message: serious or not?
software error annotation VariantAnnotation
updated 5.1 years ago by 3.9k • 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
3.1k
views
Create protein sequences including variants from a VCF file
VariantAnnotation customProDB
5.2 years ago • updated 5.1 years ago daniel.magnus.bader ▴ 40
0
votes
1
reply
939
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
834
views
writeVcf save invalid vcf with metadata out of order
variantannotation
updated 5.5 years ago by ★ 6.8k • written 5.5 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 5.9 years ago by ★ 6.8k • written 5.9 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
1.6k
views
filtering a VCF file based on genotype
variantannotation
updated 6.0 years ago by ★ 6.8k • written 6.0 years ago by ▴ 670
0
votes
1
reply
1.2k
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
6.2 years ago sandmann.t ▴ 70
2
votes
2
replies
1.4k
views
[VariantAnnotation] Preserve query metadata with locateVariants()
variantannotation locatevariants metadata mcols
updated 6.4 years ago by ★ 6.8k • written 6.4 years ago by ▴ 660
50 results • Page 1 of 1
Recent ...
Replies
Comment: Once again a "Model matrix not full rank" by arfranco ▴ 130
But.. How to run a temporal assay?
Comment: Deseq2 and Normalization of RNA sequencing data by kcarey • 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP by Gordon Smyth 50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma by Gordon Smyth 50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p- by Gordon Smyth 50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
Awards • All
Popular Question to gene_bioconductor ▴ 10
Popular Question to rohitsatyam102 ▴ 20
Popular Question to shepherl 3.9k
Popular Question to siajunren • 0
Scholar to Rory Stark ★ 5.2k
Locations • All
Italy, 2 minutes ago
WEHI, Melbourne, Australia, 4 minutes ago
United Kingdom, 5 minutes ago
University of Applied Sciences Upper Austria, Hagenberg, Austria, 9 minutes ago
The city by the bay, 27 minutes ago
Traffic: 708 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