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Showing :
variantannotation
•
reset
0
votes
2
replies
1.5k
views
merging VCF files
VariantAnnotation
VariantAnnotation
VariantAnnotation
VariantAnnotation
written 9.6 years ago by
Stephanie M. Gogarten
▴ 820
0
votes
3
replies
389
views
Problem with intronic variants in VariantAnnotation
VariantAnnotation
updated 5 months ago by
Raül
• 0 • written 7 months ago by
paolo.provero
• 0
0
votes
2
replies
307
views
Reading vcf file with readVcf
VariantAnnotation
10 months ago
aurelien.dejode
• 0
0
votes
2
replies
321
views
Multiple exons for predictCoding() from VariantAnnotation (use phase information from gff3 file)?
VariantAnnotation
updated 11 months ago by
Hervé Pagès
15k • written 13 months ago by
Kasper_holm2
• 0
0
votes
5
replies
519
views
installation error: Error in setIs(class2, cli, extensionObject = obji, doComplete = FALSE and setClass() for chromVAR and VariantAnnotation
Install
VariantAnnotation
Bioconductor
chromVAR
updated 11 months ago by
Vincent J. Carey, Jr.
6.6k • written 12 months ago by
Hannah
• 0
0
votes
1
reply
274
views
GRanges object out-of-bound
VariantAnnotation
updated 11 months ago by
Vincent J. Carey, Jr.
6.6k • written 12 months ago by
Kasper_holm2
• 0
2
votes
3
replies
437
views
readVcf(remoteFile, "hg19", "region") works on macos, fails on linux and in docker
open.BcfFile
VariantAnnotation
updated 8 months ago by
Alex
• 0 • written 13 months ago by
Paul Shannon
▴ 470
0
votes
0
replies
222
views
Annotate mutations on DNA level to splice transcripts
VariantAnnotation
13 months ago
Kasper_holm2
• 0
0
votes
4
replies
418
views
Error of read in large vcf file using readVcf
SomaticSignatures
VariantAnnotation
updated 13 months ago by
James W. MacDonald
60k • written 13 months ago by
xiw588
• 0
0
votes
2
replies
426
views
VariantAnnotation::readVcf not reading variants
VariantAnnotation
updated 15 months ago by
James W. MacDonald
60k • written 15 months ago by
peiwen.li
• 0
0
votes
2
replies
834
views
VCF File too large for tabix. Best option to make it usable with R?
samtools
tabix
VariantAnnotation
VCFArray
updated 16 months ago by
Vincent J. Carey, Jr.
6.6k • written 17 months ago by
naive
• 0
1
vote
12
replies
1.1k
views
readVcf does not recognize tabix index
VariantAnnotation
readvcf
tabix
updated 16 months ago by
Vincent J. Carey, Jr.
6.6k • written 17 months ago by
naive
• 0
0
votes
2
replies
339
views
readVCF requires the argument "genome". What does it stand for?
Genome
readVcf
VariantAnnotation
17 months ago
naive
• 0
1
vote
1
reply
497
views
Matching Variants Between Two VCF Objects
VariantAnnotation
updated 20 months ago by
nick.eagles
▴ 90 • written 20 months ago by
Dario Strbenac
★ 1.5k
2
votes
2
replies
376
views
Obtaining Comments From VCF Header
VariantAnnotation
VCFHeader
updated 2.1 years ago by
Martin Morgan
25k • written 2.1 years ago by
Dario Strbenac
★ 1.5k
3
votes
2
replies
508
views
Import or Subset VCF PASS Variants
VariantAnnotation
subset
ScanVcfParam
updated 2.3 years ago by
Martin Morgan
25k • written 2.3 years ago by
Dario Strbenac
★ 1.5k
0
votes
2
replies
408
views
Extract structural variant and flanking sequence from VCF and fasta, in R
VariantAnnotation
Bioconductor
VCF
Structural variants
R
updated 2.4 years ago by
Martin Morgan
25k • written 2.4 years ago by
W. van Rengs
• 0
0
votes
1
reply
249
views
Can strand be set to minus in VRanges objects?
VariantAnnotation
updated 2.6 years ago by
James W. MacDonald
60k • written 2.6 years ago by
david.mas
• 0
0
votes
1
reply
464
views
FilterVCF Filter '' failed: shape of 'skeleton' is not compatible with 'NROW(flesh)'
variantAnnotation
updated 2.9 years ago by
Martin Morgan
25k • written 2.9 years ago by
b.curran
• 0
2
votes
3
replies
753
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 3.1 years ago by
Steve Lianoglou
13k • written 3.1 years ago by
james.dalgleish
▴ 30
2
votes
3
replies
355
views
VariantAnnotation - subset multi-allele variants
variantAnnotation
updated 3.1 years ago by
Michael Lawrence
11k • written 3.1 years ago by
user1986
• 0
0
votes
1
reply
360
views
negative AD value interfering with readVcfasVRanges
VariantAnnotation
updated 3.2 years ago by
Michael Lawrence
11k • written 3.2 years ago by
TRASA
• 0
0
votes
3
replies
505
views
rbind VCF Two Objects Column Names Error
VariantAnnotation
VCF
3.2 years ago
Dario Strbenac
★ 1.5k
0
votes
0
replies
404
views
predictCoding warning message: serious or not?
software error
annotation
VariantAnnotation
updated 3.4 years ago by
shepherl
3.2k • written 3.4 years ago by
longsong
• 0
2
votes
3
replies
711
views
Error in VCF parsing with VariantAnnotation
software error
VariantAnnotation
ensemblVEP
updated 3.4 years ago by
Valerie Obenchain
★ 6.7k • written 3.4 years ago by
mumichae
▴ 20
3
votes
8
replies
1.2k
views
Create protein sequences including variants from a VCF file
VariantAnnotation
customProDB
3.5 years ago • updated 3.4 years ago
daniel.magnus.bader
▴ 40
0
votes
1
reply
527
views
VariantAnnotation fails to load VCF record
variantannotation
3.7 years ago
Daniel Cameron
▴ 40
0
votes
6
replies
848
views
How to prepare .vcf for seqCAT
seqCAT
variantannotation
gatk
updated 3.7 years ago by
erikfas
▴ 30 • written 3.7 years ago by
abe
• 0
0
votes
1
reply
440
views
writeVcf save invalid vcf with metadata out of order
variantannotation
updated 3.7 years ago by
Valerie Obenchain
★ 6.7k • written 3.8 years ago by
alessandro.pastore
▴ 20
1
vote
7
replies
1.7k
views
Data from ##SAMPLE lines in VCF?
variantannotation
coldata
updated 3.9 years ago by
Valerie Obenchain
★ 6.7k • written 3.9 years ago by
lvclark
▴ 10
3
votes
3
replies
673
views
Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
variantannotation
updated 4.1 years ago by
Valerie Obenchain
★ 6.7k • written 4.1 years ago by
goldberg.jm
▴ 10
3
votes
4
replies
912
views
Problem when transforming Platypus vcf to VRanges
variantannotation
vcf
readvcf
vranges
updated 4.1 years ago by
Michael Lawrence
11k • written 4.1 years ago by
david.mas
• 0
0
votes
2
replies
643
views
Error: invalid class "VRanges" object
variantannotation
VRanges
R
Rle
updated 4.1 years ago by
Valerie Obenchain
★ 6.7k • written 4.1 years ago by
Jayendra Shinde
• 0
0
votes
2
replies
712
views
VariantAnnotation::locateVariants error coming from XVector
variantannotation
xvector
iranges
4.2 years ago
Vivek.b
▴ 100
0
votes
2
replies
705
views
filtering a VCF file based on genotype
variantannotation
updated 4.2 years ago by
Valerie Obenchain
★ 6.7k • written 4.3 years ago by
Bogdan
▴ 640
0
votes
1
reply
595
views
VariantAnnotation and filtering a VCF
variantannotation
4.3 years ago
Bogdan
▴ 640
0
votes
1
reply
596
views
Annotating outdated SNP identifiers
variants
variantannotation
SNPlocs.Hsapiens.dbSNP150.GRCh38
biomaRt
4.4 years ago
sandmann.t
▴ 70
2
votes
2
replies
763
views
[VariantAnnotation] Preserve query metadata with locateVariants()
variantannotation
locatevariants
metadata
mcols
updated 4.7 years ago by
Valerie Obenchain
★ 6.7k • written 4.7 years ago by
enricoferrero
▴ 620
0
votes
2
replies
2.3k
views
Problem using biocLite() to update packages
biocLite
BiocInstaller
variantannotation
updated 4.8 years ago by
James W. MacDonald
60k • written 4.8 years ago by
Jenny Drnevich
★ 2.0k
0
votes
1
reply
755
views
predictCoding errors with: sequence ^1$ not found
variantannotation
predict coding
locateVariants
granges
4.8 years ago
tony j
• 0
7
votes
4
replies
1.4k
views
BiocGenerics built with R 3.4.2 changes behaviour
biocgenerics
iranges
variantannotation
updated 4.9 years ago by
Hervé Pagès
15k • written 4.9 years ago by
ginggs
▴ 40
7
votes
6
replies
1.1k
views
SNP location annotation problem in "VariantAnnotation" package
annotation
variantannotation
updated 4.9 years ago by
Valerie Obenchain
★ 6.7k • written 5.0 years ago by
yduan004
▴ 20
0
votes
4
replies
1.0k
views
Translation Error in predictCoding() for VariantAnnotation
VariantAnnotation
updated 4.9 years ago by
Hervé Pagès
15k • written 5.0 years ago by
creasyt
• 0
8
votes
6
replies
1.4k
views
Error when running "locateVariants" function in "VariantAnnotation" package
variantannotation
tidyverse
genomicfeatures
updated 4.9 years ago by
Hervé Pagès
15k • written 5.0 years ago by
yduan004
▴ 20
0
votes
2
replies
997
views
locateVariants function does not find an annotation for the locus
locatevariants
txdb.hsapiens.ucsc.hg19.knowngene
variantannotation
5.0 years ago
Aleksandra
• 0
0
votes
1
reply
1.0k
views
Troubleshooting a histogram DataTrack in Gviz
VariantAnnotation
gviz
5.0 years ago
Russ Fraser
▴ 20
2
votes
5
replies
1.8k
views
VariantAnnotation: Error with ScanVcfParam
variantannotation
vcf
readvcf
filtervcf
scanvcfparam
5.0 years ago
Didi
▴ 10
0
votes
2
replies
821
views
SNPs in multiple locations
txdb.hsapiens.ucsc.hg19.knowngene
ucsc
annotation
locatevariants
variantannotation
updated 5.1 years ago by
Valerie Obenchain
★ 6.7k • written 5.1 years ago by
Lna
• 0
0
votes
1
reply
592
views
summarizeVariants from VariantAnnotation reordering genes in rownames
variantannotation
summarizevariants
updated 5.1 years ago by
Valerie Obenchain
★ 6.7k • written 5.2 years ago by
Todd Creasy
• 0
3
votes
4
replies
913
views
No annotation for single SNPs
variantannotation
SNPs
txdb.hsapiens.ucsc.hg19.knowngene
ucsc
updated 5.2 years ago by
Valerie Obenchain
★ 6.7k • written 5.2 years ago by
Lna
• 0
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Comment: How should I set my eps value in cluster profiler?
by
Guido Hooiveld
★ 3.3k
Under the hood `clusterProfiler` makes use of a (fast) GSEA algorithm implemented in the package `fgsea` (function `fgseaMultilevel`). The …
Comment: Error using ChAMP SVD analysis
by
CristEin
• 0
In fact, I found that the author may have caused the problem class(myNorm) %>% length() #equals 2 class(myNorm) == "data.…
Comment: Error in Create switchAnalyzeRlist
by
k.vitting.seerup
▴ 120
Oh sorry I missed the species. Yes they also match for chicken :-) (both being called "ENSGALT..."). The other is from NCBI
Comment: Error in Create switchAnalyzeRlist
by
bpshtiwan
▴ 10
Ok, have you looked cDNA fasta file for Chicken (maternal Broiler) Gallus gallus? I am using Kallisto for alignment and quantification. He…
Comment: DEXseq error unable to find an inherited method for function NSBS for signature
by
ta_awwad
▴ 10
Hi there, did you manage to solve this problem? thanks TA
Votes
DEXseq error unable to find an inherited method for function NSBS for signature CompressedIntegerList
Answer: Error in Create switchAnalyzeRlist
Answer: Error in Create switchAnalyzeRlist
A: DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Ge
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
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