Showing : variantAnnotation • reset
0
votes
2
replies
1.7k
views
VariantAnnotation::locateVariants error coming from XVector
variantannotation xvector iranges
7.6 years ago • updated 7.5 years ago Vivek.b ▴ 100
0
votes
2
replies
2.4k
views
filtering a VCF file based on genotype
variantannotation
updated 7.6 years ago by ★ 6.8k • written 7.6 years ago by ▴ 670
0
votes
1
reply
1.8k
views
VariantAnnotation and filtering a VCF
variantannotation
7.6 years ago Bogdan ▴ 670
0
votes
1
reply
1.6k
views
Annotating outdated SNP identifiers
variants variantannotation SNPlocs.Hsapiens.dbSNP150.GRCh38 biomaRt
7.8 years ago sandmann.t ▴ 70
2
votes
2
replies
2.0k
views
[VariantAnnotation] Preserve query metadata with locateVariants()
variantannotation locatevariants metadata mcols
updated 8.0 years ago by ★ 6.8k • written 8.0 years ago by ▴ 680
0
votes
2
replies
3.4k
views
Problem using biocLite() to update packages
biocLite BiocInstaller variantannotation
updated 8.1 years ago by 68k • written 8.1 years ago by ★ 2.0k
0
votes
1
reply
1.5k
views
predictCoding errors with: sequence ^1$ not found
variantannotation predict coding locateVariants granges
8.1 years ago tony j • 0
7
votes
4
replies
2.8k
views
BiocGenerics built with R 3.4.2 changes behaviour
biocgenerics iranges variantannotation
updated 8.2 years ago by 16k • written 8.2 years ago by ▴ 40
7
votes
6
replies
2.4k
views
SNP location annotation problem in "VariantAnnotation" package
annotation variantannotation
updated 8.3 years ago by ★ 6.8k • written 8.3 years ago by ▴ 20
0
votes
4
replies
1.9k
views
Translation Error in predictCoding() for VariantAnnotation
VariantAnnotation
updated 8.3 years ago by 16k • written 8.3 years ago by • 0
8
votes
6
replies
2.7k
views
Error when running "locateVariants" function in "VariantAnnotation" package
variantannotation tidyverse genomicfeatures
updated 8.3 years ago by 16k • written 8.3 years ago by ▴ 20
0
votes
2
replies
2.1k
views
locateVariants function does not find an annotation for the locus
locatevariants txdb.hsapiens.ucsc.hg19.knowngene variantannotation
8.3 years ago Aleksandra • 0
0
votes
1
reply
1.8k
views
Troubleshooting a histogram DataTrack in Gviz
VariantAnnotation gviz
8.4 years ago Russ Fraser ▴ 40
2
votes
5
replies
3.4k
views
VariantAnnotation: Error with ScanVcfParam
variantannotation vcf readvcf filtervcf scanvcfparam
8.4 years ago Didi ▴ 10
0
votes
2
replies
2.0k
views
SNPs in multiple locations
txdb.hsapiens.ucsc.hg19.knowngene ucsc annotation locatevariants variantannotation
updated 8.5 years ago by ★ 6.8k • written 8.5 years ago by • 0
0
votes
1
reply
1.1k
views
summarizeVariants from VariantAnnotation reordering genes in rownames
variantannotation summarizevariants
updated 8.5 years ago by ★ 6.8k • written 8.5 years ago by • 0
3
votes
4
replies
2.0k
views
No annotation for single SNPs
variantannotation SNPs txdb.hsapiens.ucsc.hg19.knowngene ucsc
updated 8.5 years ago by ★ 6.8k • written 8.5 years ago by • 0
0
votes
6
replies
3.1k
views
Error using readVcf
gwastools variantannotation
updated 8.5 years ago by ▴ 890 • written 8.5 years ago by • 0
3
votes
3
replies
3.0k
views
VariantAnnotation Installation Failure
VariantAnnotation
updated 8.6 years ago by ★ 6.8k • written 8.6 years ago by ▴ 370
1
vote
2
replies
1.2k
views
Exclude Mutations from Mutation List
variantannotation
updated 8.6 years ago by 25k • written 8.6 years ago by ▴ 110
2
votes
6
replies
3.5k
views
extracting Allele Read Counts - part2
rsamtools variantannotation
updated 8.7 years ago by 68k • written 8.7 years ago by ▴ 670
0
votes
3
replies
1.5k
views
Error in c(DataFrameList(META = meta), tbls[unique(tags)])
VariantAnnotation
updated 8.7 years ago by 16k • written 8.7 years ago by • 0
1
vote
3
replies
2.6k
views
annotation of SV (Structural Variants)
variantannotation annotationhub
8.7 years ago Bogdan ▴ 670
3
votes
2
replies
2.0k
views
filtering VCF files
variantannotation variantfiltering
updated 8.7 years ago by ★ 11k • written 8.7 years ago by ▴ 670
0
votes
0
replies
1.3k
views
VariantAnnotation mapToTranscripts: best implementation
VariantAnnotation mapToTranscripts
8.8 years ago kristina_holton • 0
0
votes
2
replies
1.4k
views
does readVcf mistakenly ignore ploidy for missing genotypes?
readvcf gt missing VariantAnnotation
8.8 years ago TimothéeFlutre ▴ 80
2
votes
7
replies
2.7k
views
VariantAnnotation - expand not working as intended for VCF
variantannotation
updated 8.9 years ago by ★ 11k • written 8.9 years ago by • 0
2
votes
4
replies
2.7k
views
Best way to create a VRanges object from a large VCF file?
variantannotation readvcf readvcfasvranges vcf
updated 8.9 years ago by ★ 11k • written 8.9 years ago by • 0
3
votes
3
replies
1.9k
views
CollapsedVCF and ExpandedVCF rownames and vcfs with large ref/alt columns
variantannotation VCF
updated 9.0 years ago by ★ 6.8k • written 9.0 years ago by 21k
0
votes
2
replies
1.8k
views
Problem with VariantAnnotation and VCF "R" genotype fields when expanding CollapsedVCF
VariantAnnotation bug
updated 9.0 years ago by ★ 6.8k • written 9.0 years ago by 21k
1
vote
3
replies
1.8k
views
VariantAnnotation error with readVcf after genotypeToSnpMatrix
variantannotation
9.1 years ago sarah.williams1 ▴ 40
0
votes
0
replies
1.5k
views
Job: PhD Position in Bioinformatics
bioinformatics protein variantannotation data integration Job
9.1 years ago stephan.pabinger • 0
0
votes
1
reply
1.3k
views
VariantAnnotation -filterVcf/FilterRules - 3 fxns as list to FilterRules throughs and erro
filtervcf variantannotation
updated 9.1 years ago by 25k • written 9.1 years ago by ▴ 60
1
vote
23
replies
3.8k
views
Distance calculation for variants in intergenic regions
locatevariants variantannotation genomicfeatures
updated 9.1 years ago by ★ 11k • written 9.1 years ago by • 0
0
votes
7
replies
1.7k
views
VariantAnnotation - filterVcf - Prints multiple vcf headers
variantannotation
updated 9.1 years ago by 25k • written 9.1 years ago by ▴ 60
0
votes
23
replies
3.8k
views
VariantAnnotation geno function
variantannotation
9.1 years ago ribioinfo ▴ 100
3
votes
9
replies
4.2k
views
Annotate VCFs with Cosmic (ExAC etc.) fields
variantannotation cosmic exac
updated 9.1 years ago by 25k • written 9.1 years ago by ▴ 130
0
votes
2
replies
1.5k
views
Create VRanges object from mutation data (txt extracted from annotated vcf)
iranges variantannotation
updated 9.2 years ago by ★ 11k • written 9.2 years ago by • 0
2
votes
3
replies
2.0k
views
predictCoding fails with error
VariantAnnotation
9.2 years ago Stephane Plaisance | VIB | ▴ 60
1
vote
2
replies
1.3k
views
VariantAnnotation CollapsedVCF trouble
variantannotation subsetting
9.2 years ago Fabian Grammes ▴ 20
0
votes
1
reply
1.5k
views
SNP Injection in Custom BSGenome
variantannotation bsgenome
updated 9.3 years ago by 16k • written 9.3 years ago by • 0
1
vote
2
replies
1.5k
views
Locating enhancers that are mutated
snv granges genomicranges variantannotation indel
updated 9.3 years ago by ★ 11k • written 9.3 years ago by • 0
0
votes
0
replies
1.1k
views
After mapping one Sanger sequence read (about 900bp) to hg19 using blastn, How can I get variants presented as reference-based position and base ch…
Biostrings blast variantannotation
9.3 years ago li lilingdu ▴ 450
1
vote
9
replies
1.9k
views
Problem with summarizeVariants function (VariantAnnotation) when using a multi-sample vcf
variantannotation
updated 9.3 years ago by ★ 6.8k • written 9.4 years ago by • 0
0
votes
1
reply
1.2k
views
VariantAnnotation print malformated vcf
variantannotation writevcf
updated 9.4 years ago by ★ 6.8k • written 9.4 years ago by • 0
5
votes
2
replies
1.7k
views
info(header(vcf)) remembers fields not imported: bugfix?
VariantAnnotation
9.4 years ago kevin.rue ▴ 350
2
votes
2
replies
1.7k
views
readVCFAsVRanges in VariantAnnotation broken by an FTZ format?
variantannotation readvcfasvranges vcf
updated 9.4 years ago by ★ 11k • written 9.4 years ago by ▴ 120
4
votes
10
replies
4.0k
views
Best way to import from multiple VCF files?
variantannotation
updated 9.4 years ago by 4.2k • written 9.4 years ago by ▴ 150
1
vote
2
replies
1.6k
views
Expand annotation on a vcf file
vcf variantannotation
updated 9.4 years ago by ★ 11k • written 9.4 years ago by • 0
3
votes
8
replies
2.6k
views
Vcf to VRanges conversion error: ["incorrect number of dimensions"]
variantannotation somaticsignatures
updated 9.4 years ago by ★ 11k • written 9.4 years ago by • 0
217 results • Page 2 of 5
Recent ...
Replies
Comment: Bioinformatician at the Lausanne University Hospital by eja.ger.m • 0
For individuals looking to improve communication and collaboration in demanding medical or research environments like the Genetic Medicine …
Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Awards • All
Popular Question to Lluís Revilla Sancho ▴ 760
Popular Question to James W. MacDonald 68k
Popular Question to shepherl 4.2k
Popular Question to Gordon Smyth 53k
Commentator to sina.nassiri ▴ 130
Locations • All
United States, 30 minutes ago
United States, 31 minutes ago
The city by the bay, 38 minutes ago
United States, 1 hour ago
United States, 3 hours ago
Traffic: 1435 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