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VariantAnnotation
•
reset
0
votes
23
replies
2.6k
views
VariantAnnotation geno function
variantannotation
7.5 years ago
ribioinfo
▴ 100
1
vote
23
replies
2.4k
views
Distance calculation for variants in intergenic regions
locatevariants
variantannotation
genomicfeatures
updated 7.5 years ago by
Michael Lawrence
★ 11k • written 7.5 years ago by
Lna
• 0
0
votes
21
replies
4.3k
views
VariantAnnotation Errors and void outputs
variantannotation
readvcf
9.0 years ago
pifferdavide
• 0
0
votes
20
replies
2.3k
views
VariantAnnotation function getTranscriptSeqs() gives error "object '.makeUCSCTxListFromGRangesList' not found"
variantannotation
8.7 years ago • updated 8.5 years ago
Tjeerd Dijkstra
• 0
0
votes
17
replies
2.6k
views
problems with strand in predictCoding
VariantAnnotation
Annotation
BSgenome
BSgenome
VariantAnnotation
VariantAnnotation
BSgenome
updated 12.0 years ago by
bnorthoff@web.de
▴ 20 • written 12.0 years ago by
Jeremiah Degenhardt
▴ 50
1
vote
12
replies
2.8k
views
VariantAnnotation: no method for function 'path' for signature 'character'
variantannotation
readvcf
readgt
updated 9.4 years ago by
Valerie Obenchain
★ 6.8k • written 9.4 years ago by
Kipper Fletez-Brant
▴ 150
1
vote
12
replies
3.0k
views
readVcf does not recognize tabix index
VariantAnnotation
readvcf
tabix
updated 3.1 years ago by
Vincent J. Carey, Jr.
6.7k • written 3.1 years ago by
naive
• 0
4
votes
11
replies
1.8k
views
Filter every X position
variantannotation
9.4 years ago • updated 9.3 years ago
remi.tournebize
▴ 10
0
votes
11
replies
2.0k
views
Complete variant toolbox: gmapR/VariantTools/VariantAnnotation
VariantAnnotation
Annotation
VariantAnnotation
VariantTools
VariantAnnotation
Annotation
updated 10.4 years ago by
Valerie Obenchain
★ 6.8k • written 10.4 years ago by
Thomas Girke
★ 1.7k
1
vote
10
replies
2.3k
views
predictCoding error DNAStringSet_translate
variantannotation
predict coding
updated 9.1 years ago by
Valerie Obenchain
★ 6.8k • written 9.1 years ago by
Miss Agnieszka Aleksandra Golicz
▴ 40
4
votes
10
replies
2.9k
views
Best way to import from multiple VCF files?
variantannotation
updated 7.8 years ago by
shepherl
3.9k • written 7.8 years ago by
Kipper Fletez-Brant
▴ 150
0
votes
10
replies
2.8k
views
Incorrect row names when a VCF has multiple ALTs.
variantannotation
vcf
updated 9.5 years ago by
Valerie Obenchain
★ 6.8k • written 9.5 years ago by
bicycle1885
• 0
2
votes
9
replies
2.7k
views
ReadVCF not reading samples
readvcf
vcf
variantannotation
9.0 years ago
askates
▴ 10
1
vote
9
replies
1.3k
views
Problem with summarizeVariants function (VariantAnnotation) when using a multi-sample vcf
variantannotation
updated 7.7 years ago by
Valerie Obenchain
★ 6.8k • written 7.7 years ago by
juls
• 0
3
votes
9
replies
3.1k
views
Annotate VCFs with Cosmic (ExAC etc.) fields
variantannotation
cosmic
exac
updated 7.5 years ago by
Martin Morgan
25k • written 7.5 years ago by
markus.riester
▴ 130
0
votes
9
replies
1.9k
views
variantAnnotation: alternative GENETIC_CODE, and circular chromosomes?
VariantAnnotation
Cancer
Yeast
annotate
Biostrings
VariantAnnotation
VariantAnnotation
updated 10.3 years ago by
Hervé Pagès
16k • written 10.3 years ago by
Janet Young
▴ 740
3
votes
8
replies
1.9k
views
Vcf to VRanges conversion error: ["incorrect number of dimensions"]
variantannotation
somaticsignatures
updated 7.8 years ago by
Michael Lawrence
★ 11k • written 7.8 years ago by
maria.vila
• 0
3
votes
8
replies
3.1k
views
Create protein sequences including variants from a VCF file
VariantAnnotation
customProDB
5.2 years ago
daniel.magnus.bader
▴ 40
0
votes
8
replies
2.8k
views
Best practices to find intersection among variants
VariantAnnotation
genomes
VariantAnnotation
VariantAnnotation
genomes
VariantAnnotation
updated 9.7 years ago by
Julian Gehring
★ 1.3k • written 9.7 years ago by
Marco Blanchette
▴ 220
4
votes
8
replies
1.5k
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
1
vote
8
replies
1.2k
views
writeVCF outputs invalid VCF if no genotypes
variantannotation
updated 8.8 years ago by
Valerie Obenchain
★ 6.8k • written 8.8 years ago by
Daniel Cameron
▴ 40
0
votes
7
replies
2.8k
views
VariantAnnotation: Performance and memory issues in readVcf
VariantAnnotation
PROcess
Rsamtools
VariantAnnotation
VariantAnnotation
PROcess
Rsamtools
updated 11.0 years ago by
Vincent J. Carey, Jr.
6.7k • written 11.0 years ago by
UBod
▴ 290
1
vote
7
replies
3.1k
views
Data from ##SAMPLE lines in VCF?
variantannotation
coldata
updated 5.6 years ago by
Valerie Obenchain
★ 6.8k • written 5.6 years ago by
lvclark
▴ 10
0
votes
7
replies
1.7k
views
mutant allele read counts
VariantAnnotation
VariantAnnotation
VariantAnnotation
VariantAnnotation
updated 9.9 years ago by
Valerie Obenchain
★ 6.8k • written 9.9 years ago by
Guest User
★ 13k
2
votes
7
replies
1.9k
views
VariantAnnotation - expand not working as intended for VCF
variantannotation
updated 7.3 years ago by
Michael Lawrence
★ 11k • written 7.3 years ago by
sebastian.hollizeck
• 0
0
votes
7
replies
1.7k
views
VariantAnnotation produces duplicate names
variantannotation
updated 8.1 years ago by
Valerie Obenchain
★ 6.8k • written 8.1 years ago by
Daniel Cameron
▴ 40
0
votes
7
replies
2.8k
views
append to bgzipped VCF file
variantannotation
tabix
updated 8.5 years ago by
Michael Lawrence
★ 11k • written 8.5 years ago by
TimothéeFlutre
▴ 80
0
votes
7
replies
1.2k
views
VariantAnnotation - filterVcf - Prints multiple vcf headers
variantannotation
updated 7.5 years ago by
Martin Morgan
25k • written 7.5 years ago by
stephen sefick
▴ 60
0
votes
6
replies
1.6k
views
How to prepare .vcf for seqCAT
seqCAT
variantannotation
gatk
updated 5.4 years ago by
erikfas
▴ 30 • written 5.4 years ago by
abe
• 0
8
votes
6
replies
2.0k
views
Error when running "locateVariants" function in "VariantAnnotation" package
variantannotation
tidyverse
genomicfeatures
updated 6.7 years ago by
Hervé Pagès
16k • written 6.7 years ago by
yduan004
▴ 20
2
votes
6
replies
2.6k
views
extracting Allele Read Counts - part2
rsamtools
variantannotation
updated 7.1 years ago by
James W. MacDonald
65k • written 7.1 years ago by
Bogdan
▴ 670
0
votes
6
replies
2.2k
views
Error using readVcf
gwastools
variantannotation
updated 6.9 years ago by
Stephanie M. Gogarten
▴ 870 • written 6.9 years ago by
Lna
• 0
5
votes
6
replies
3.2k
views
Error in reading 1000 genomes data
variantannotation
updated 8.2 years ago by
Martin Morgan
25k • written 9.5 years ago by
Wade Copeland
▴ 20
7
votes
6
replies
1.8k
views
SNP location annotation problem in "VariantAnnotation" package
annotation
variantannotation
updated 6.7 years ago by
Valerie Obenchain
★ 6.8k • written 6.7 years ago by
yduan004
▴ 20
0
votes
6
replies
2.7k
views
readVcf shape of 'skeleton' is not compatible with 'NROW(flesh)'
variantannotation
updated 8.9 years ago by
Valerie Obenchain
★ 6.8k • written 8.9 years ago by
Miss Agnieszka Aleksandra Golicz
▴ 40
2
votes
6
replies
3.3k
views
Import of vcf with VariantAnnotation
variantannotation
somaticsignatures
9.5 years ago
Anna N.
• 0
0
votes
6
replies
1.4k
views
Why is writeVcf() slow?
VariantAnnotation
VariantAnnotation
VariantAnnotation
VariantAnnotation
updated 11.5 years ago by
Valerie Obenchain
★ 6.8k • written 11.5 years ago by
Peter Hickey
▴ 740
4
votes
6
replies
1.9k
views
VariantAnnotation non-model species
variantannotation
9.2 years ago
Miss Agnieszka Aleksandra Golicz
▴ 40
0
votes
5
replies
1.7k
views
VariantAnnotation and distance to genes
VariantAnnotation
VariantAnnotation
VariantAnnotation
VariantAnnotation
updated 11.0 years ago by
James W. MacDonald
65k • written 11.0 years ago by
Gad Abraham
▴ 20
0
votes
5
replies
2.0k
views
VariantAnnotation _ problem in merging files, mutationspectrum per sample
variantannotation
updated 9.4 years ago by
Julian Gehring
★ 1.3k • written 9.4 years ago by
Anna N.
• 0
0
votes
5
replies
1.7k
views
VariantAnnotation VCF read error
variantannotation
readvcf
updated 9.5 years ago by
Valerie Obenchain
★ 6.8k • written 9.5 years ago by
JK
▴ 10
4
votes
5
replies
1.3k
views
parRapply in BiocParallel ?
biocparallel
variantannotation
updated 7.9 years ago by
Michael Lawrence
★ 11k • written 7.9 years ago by
kevin.rue
▴ 350
0
votes
5
replies
1.2k
views
Complete variant toolbox: gmapR/VariantTools/VariantAnnotation - revived
VariantAnnotation
GenomicRanges
VariantAnnotation
VariantAnnotation
GenomicRanges
updated 9.8 years ago by
Robert Castelo
★ 3.3k • written 9.8 years ago by
Valerie Obenchain
★ 6.8k
7
votes
5
replies
1.3k
views
writeVcf no longer writes records for ungenotyped data
variantannotation
updated 9.5 years ago by
Valerie Obenchain
★ 6.8k • written 9.5 years ago by
Daniel Cameron
▴ 40
1
vote
5
replies
4.3k
views
Converting a DNAStringSetList to characters quickly
readVcf
DNAStringSet
DNAStringSetList
variantannotation
readvcf
9.0 years ago
dan.gatti
• 0
0
votes
5
replies
2.1k
views
Error installing VariantAnnotation with bioconductor/devel_core
install
variantannotation
9.2 years ago
kforner
• 0
2
votes
5
replies
2.6k
views
VariantAnnotation: Error with ScanVcfParam
variantannotation
vcf
readvcf
filtervcf
scanvcfparam
6.8 years ago
Didi
▴ 10
0
votes
5
replies
1.8k
views
Complete variant toolbox: gmapR/VariantTools/VariantAnnotation
BiocViews
VariantAnnotation
Annotation
biocViews
Rsubread
VariantAnnotation
gmapR
BiocViews
10.4 years ago
Thomas Girke
★ 1.7k
3
votes
5
replies
1.5k
views
filterVcf: crash with isSNV() filter argument
VariantAnnotation
filterVcf
8.8 years ago • updated 8.7 years ago
pau.puigdevall
• 0
3
votes
5
replies
3.0k
views
Add Custom Annotations to Multi-Sample VCF with VariantAnnotation() package
variantannotation
granges
DNAStringSetList
findoverlaps
Vranges
9.2 years ago
summerela
• 0
50 results • Page
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