Showing : variantannotation • reset
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2
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133
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Docker usage with Trio Bioconductor Package
VariantAnnotation docker trio
updated 24 days ago by ★ 2.9k • written 24 days ago by • 0
4
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8
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472
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
11 weeks ago davidhillis • 0
0
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0
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189
views
VariantAnnotation::readVcf incorrectly processes GATK Mutect2 vcf INFO field AS_SB_TABLE
vcf AS_SB_TABLE readVcf Mutect2 VariantAnnotation
3 months ago therealgenna • 0
0
votes
3
replies
363
views
Add GP values to VCF
VariantAnnotation
4 months ago Stephanie M. Gogarten ▴ 840
0
votes
1
reply
608
views
Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123 VariantFiltering Alignment VariantAnnotation
updated 7 months ago by 63k • written 7 months ago by ▴ 10
2
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4
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445
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
8 months ago rwan.work • 0
0
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2
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288
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
8 months ago rwan.work • 0
0
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3
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672
views
Problem with intronic variants in VariantAnnotation
VariantAnnotation
updated 15 months ago by • 0 • written 17 months ago by • 0
0
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2
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554
views
Reading vcf file with readVcf
VariantAnnotation
20 months ago aurelien.dejode • 0
0
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5
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822
views
installation error: Error in setIs(class2, cli, extensionObject = obji, doComplete = FALSE and setClass() for chromVAR and VariantAnnotation
Install VariantAnnotation Bioconductor chromVAR
updated 21 months ago by 6.6k • written 21 months ago by • 0
0
votes
1
reply
505
views
GRanges object out-of-bound
VariantAnnotation
updated 21 months ago by 6.6k • written 22 months ago by • 0
0
votes
2
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481
views
Multiple exons for predictCoding() from VariantAnnotation (use phase information from gff3 file)?
VariantAnnotation
updated 21 months ago by 16k • written 22 months ago by • 0
0
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0
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361
views
Annotate mutations on DNA level to splice transcripts
VariantAnnotation
23 months ago • updated 22 months ago Kasper_holm2 • 0
2
votes
3
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669
views
readVcf(remoteFile, "hg19", "region") works on macos, fails on linux and in docker
open.BcfFile VariantAnnotation
updated 18 months ago by • 0 • written 23 months ago by ▴ 470
0
votes
4
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841
views
Error of read in large vcf file using readVcf
SomaticSignatures VariantAnnotation
updated 23 months ago by 63k • written 23 months ago by • 0
0
votes
2
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747
views
VariantAnnotation::readVcf not reading variants
VariantAnnotation
updated 2.0 years ago by 63k • written 2.0 years ago by • 0
1
vote
12
replies
1.9k
views
readVcf does not recognize tabix index
VariantAnnotation readvcf tabix
updated 2.2 years ago by 6.6k • written 2.2 years ago by • 0
0
votes
2
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705
views
readVCF requires the argument "genome". What does it stand for?
Genome readVcf VariantAnnotation
2.2 years ago naive • 0
0
votes
2
replies
1.5k
views
VCF File too large for tabix. Best option to make it usable with R?
samtools tabix VariantAnnotation VCFArray
updated 2.2 years ago by 6.6k • written 2.3 years ago by • 0
2
votes
1
reply
777
views
Matching Variants Between Two VCF Objects
VariantAnnotation
updated 2.5 years ago by ▴ 100 • written 2.5 years ago by ★ 1.5k
2
votes
2
replies
698
views
Obtaining Comments From VCF Header
VariantAnnotation VCFHeader
updated 2.9 years ago by 25k • written 2.9 years ago by ★ 1.5k
3
votes
2
replies
804
views
Import or Subset VCF PASS Variants
VariantAnnotation subset ScanVcfParam
updated 3.1 years ago by 25k • written 3.1 years ago by ★ 1.5k
0
votes
2
replies
713
views
Extract structural variant and flanking sequence from VCF and fasta, in R
VariantAnnotation Bioconductor VCF Structural variants R
updated 3.2 years ago by 25k • written 3.2 years ago by • 0
0
votes
1
reply
373
views
Can strand be set to minus in VRanges objects?
VariantAnnotation
updated 3.4 years ago by 63k • written 3.4 years ago by • 0
0
votes
1
reply
715
views
FilterVCF Filter '' failed: shape of 'skeleton' is not compatible with 'NROW(flesh)'
variantAnnotation
updated 3.7 years ago by 25k • written 3.7 years ago by • 0
2
votes
3
replies
1.0k
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 3.9 years ago by 13k • written 3.9 years ago by ▴ 30
2
votes
3
replies
550
views
VariantAnnotation - subset multi-allele variants
variantAnnotation
updated 3.9 years ago by 11k • written 3.9 years ago by • 0
0
votes
1
reply
497
views
negative AD value interfering with readVcfasVRanges
VariantAnnotation
updated 4.0 years ago by 11k • written 4.0 years ago by • 0
0
votes
3
replies
682
views
rbind VCF Two Objects Column Names Error
VariantAnnotation VCF
4.0 years ago Dario Strbenac ★ 1.5k
0
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0
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530
views
predictCoding warning message: serious or not?
software error annotation VariantAnnotation
updated 4.2 years ago by 3.5k • written 4.2 years ago by • 0
2
votes
3
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990
views
Error in VCF parsing with VariantAnnotation
software error VariantAnnotation ensemblVEP
updated 4.2 years ago by ★ 6.8k • written 4.2 years ago by ▴ 20
3
votes
8
replies
2.0k
views
Create protein sequences including variants from a VCF file
VariantAnnotation customProDB
4.3 years ago • updated 4.2 years ago daniel.magnus.bader ▴ 40
0
votes
1
reply
700
views
VariantAnnotation fails to load VCF record
variantannotation
4.5 years ago Daniel Cameron ▴ 40
0
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6
replies
1.1k
views
How to prepare .vcf for seqCAT
seqCAT variantannotation gatk
updated 4.5 years ago by ▴ 30 • written 4.5 years ago by • 0
0
votes
1
reply
585
views
writeVcf save invalid vcf with metadata out of order
variantannotation
updated 4.5 years ago by ★ 6.8k • written 4.6 years ago by ▴ 20
1
vote
7
replies
2.4k
views
Data from ##SAMPLE lines in VCF?
variantannotation coldata
updated 4.7 years ago by ★ 6.8k • written 4.7 years ago by ▴ 10
3
votes
4
replies
1.2k
views
Problem when transforming Platypus vcf to VRanges
variantannotation vcf readvcf vranges
updated 4.9 years ago by 11k • written 4.9 years ago by • 0
3
votes
3
replies
890
views
Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
variantannotation
updated 4.9 years ago by ★ 6.8k • written 4.9 years ago by ▴ 10
0
votes
2
replies
839
views
Error: invalid class "VRanges" object
variantannotation VRanges R Rle
updated 4.9 years ago by ★ 6.8k • written 4.9 years ago by • 0
0
votes
2
replies
909
views
VariantAnnotation::locateVariants error coming from XVector
variantannotation xvector iranges
5.0 years ago Vivek.b ▴ 100
0
votes
2
replies
1.1k
views
filtering a VCF file based on genotype
variantannotation
updated 5.1 years ago by ★ 6.8k • written 5.1 years ago by ▴ 660
0
votes
1
reply
776
views
VariantAnnotation and filtering a VCF
variantannotation
5.1 years ago Bogdan ▴ 660
0
votes
1
reply
784
views
Annotating outdated SNP identifiers
variants variantannotation SNPlocs.Hsapiens.dbSNP150.GRCh38 biomaRt
5.3 years ago sandmann.t ▴ 70
2
votes
2
replies
985
views
[VariantAnnotation] Preserve query metadata with locateVariants()
variantannotation locatevariants metadata mcols
updated 5.5 years ago by ★ 6.8k • written 5.5 years ago by ▴ 660
0
votes
2
replies
2.5k
views
Problem using biocLite() to update packages
biocLite BiocInstaller variantannotation
updated 5.6 years ago by 63k • written 5.6 years ago by ★ 2.0k
0
votes
1
reply
929
views
predictCoding errors with: sequence ^1$ not found
variantannotation predict coding locateVariants granges
5.6 years ago tony j • 0
7
votes
4
replies
1.7k
views
BiocGenerics built with R 3.4.2 changes behaviour
biocgenerics iranges variantannotation
updated 5.7 years ago by 16k • written 5.7 years ago by ▴ 40
8
votes
6
replies
1.6k
views
Error when running "locateVariants" function in "VariantAnnotation" package
variantannotation tidyverse genomicfeatures
updated 5.7 years ago by 16k • written 5.8 years ago by ▴ 20
7
votes
6
replies
1.4k
views
SNP location annotation problem in "VariantAnnotation" package
annotation variantannotation
updated 5.7 years ago by ★ 6.8k • written 5.8 years ago by ▴ 20
0
votes
4
replies
1.3k
views
Translation Error in predictCoding() for VariantAnnotation
VariantAnnotation
updated 5.7 years ago by 16k • written 5.8 years ago by • 0
50 results • Page 1 of 1
Recent ...
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Answer: Ensembl plants at annotationHub? by Bruno • 0
Hi Johannes, First, thank you so much for providing these annotations for the community. We feel often a bit left off in the plant commu…
Comment: DESeq2 on multilevel design variable by swbarnes2 ★ 1.2k
Did you relevel before or after calling DESeq?
Comment: SummarizedExperiment is now warning on attach about `read_block` namespace confl by Hervé Pagès 16k
Available since last Friday. See https://bioconductor.org/packages/3.17/DelayedArray
Comment: Diffbind "No genome detected" by James W. MacDonald 63k
The error you see comes from an internal function called `pv.genome` that inspects the header of your BAM file and tries to infer the genom…
Comment: Diffbind "No genome detected" by kyliecode • 0
Hi James, Thanks for your reply! For the blacklist, I just used the one provided by DiffBind, which is "DBA_BLACKLIST_MM10". For the grey…
Votes
Answer: DESeq2 on multilevel design variable
Comment: Sudden error with KEGG analysis using gometh
Comment: Sudden error with KEGG analysis using gometh
Answer: Although I successfully installed the package "simpleaffy'' , I cannot library i
Answer: Annotation with org.Hs.eg.db Genome Build 38
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