Showing : VariantAnnotation • reset
0
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2
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126
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Problem with intronic variants in VariantAnnotation
VariantAnnotation
updated 11 days ago by 6.5k • written 19 days ago by • 0
0
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2
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196
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Reading vcf file with readVcf
VariantAnnotation
4 months ago aurelien.dejode • 0
0
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2
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218
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Multiple exons for predictCoding() from VariantAnnotation (use phase information from gff3 file)?
VariantAnnotation
updated 4 months ago by 15k • written 6 months ago by • 0
0
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5
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355
views
installation error: Error in setIs(class2, cli, extensionObject = obji, doComplete = FALSE and setClass() for chromVAR and VariantAnnotation
Install VariantAnnotation Bioconductor chromVAR
updated 5 months ago by 6.5k • written 5 months ago by • 0
0
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1
reply
137
views
GRanges object out-of-bound
VariantAnnotation
updated 4 months ago by 6.5k • written 6 months ago by • 0
2
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3
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315
views
readVcf(remoteFile, "hg19", "region") works on macos, fails on linux and in docker
open.BcfFile VariantAnnotation
updated 7 weeks ago by • 0 • written 6 months ago by ▴ 460
0
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0
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140
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Annotate mutations on DNA level to splice transcripts
VariantAnnotation
6 months ago Kasper_holm2 • 0
0
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4
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234
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Error of read in large vcf file using readVcf
SomaticSignatures VariantAnnotation
updated 6 months ago by 58k • written 6 months ago by • 0
0
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2
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280
views
VariantAnnotation::readVcf not reading variants
VariantAnnotation
updated 8 months ago by 58k • written 8 months ago by • 0
0
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2
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461
views
VCF File too large for tabix. Best option to make it usable with R?
samtools tabix VariantAnnotation VCFArray
updated 9 months ago by 6.5k • written 10 months ago by • 0
1
vote
12
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740
views
readVcf does not recognize tabix index
VariantAnnotation readvcf tabix
updated 9 months ago by 6.5k • written 10 months ago by • 0
0
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2
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211
views
readVCF requires the argument "genome". What does it stand for?
Genome readVcf VariantAnnotation
10 months ago naive • 0
1
vote
1
reply
312
views
Matching Variants Between Two VCF Objects
VariantAnnotation
updated 13 months ago by ▴ 90 • written 14 months ago by ★ 1.5k
2
votes
2
replies
267
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Obtaining Comments From VCF Header
VariantAnnotation VCFHeader
updated 19 months ago by 25k • written 19 months ago by ★ 1.5k
3
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2
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328
views
Import or Subset VCF PASS Variants
VariantAnnotation subset ScanVcfParam
updated 21 months ago by 25k • written 21 months ago by ★ 1.5k
0
votes
2
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260
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Extract structural variant and flanking sequence from VCF and fasta, in R
VariantAnnotation Bioconductor VCF Structural variants R
updated 21 months ago by 25k • written 21 months ago by • 0
0
votes
1
reply
171
views
Can strand be set to minus in VRanges objects?
VariantAnnotation
updated 2.0 years ago by 58k • written 2.0 years ago by • 0
0
votes
1
reply
362
views
FilterVCF Filter '' failed: shape of 'skeleton' is not compatible with 'NROW(flesh)'
variantAnnotation
updated 2.3 years ago by 25k • written 2.3 years ago by • 0
2
votes
3
replies
574
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 2.5 years ago by 13k • written 2.5 years ago by ▴ 30
2
votes
3
replies
287
views
VariantAnnotation - subset multi-allele variants
variantAnnotation
updated 2.5 years ago by 11k • written 2.5 years ago by • 0
0
votes
1
reply
285
views
negative AD value interfering with readVcfasVRanges
VariantAnnotation
updated 2.6 years ago by 11k • written 2.6 years ago by • 0
0
votes
3
replies
418
views
rbind VCF Two Objects Column Names Error
VariantAnnotation VCF
2.6 years ago Dario Strbenac ★ 1.5k
0
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0
replies
328
views
predictCoding warning message: serious or not?
software error annotation VariantAnnotation
updated 2.8 years ago by 2.9k • written 2.8 years ago by • 0
2
votes
3
replies
543
views
Error in VCF parsing with VariantAnnotation
software error VariantAnnotation ensemblVEP
updated 2.9 years ago by ★ 6.7k • written 2.9 years ago by ▴ 20
3
votes
8
replies
774
views
Create protein sequences including variants from a VCF file
VariantAnnotation customProDB
2.9 years ago daniel.magnus.bader ▴ 40
0
votes
1
reply
450
views
VariantAnnotation fails to load VCF record
variantannotation
3.1 years ago Daniel Cameron ▴ 20
0
votes
6
replies
711
views
How to prepare .vcf for seqCAT
seqCAT variantannotation gatk
updated 3.1 years ago by ▴ 30 • written 3.1 years ago by • 0
0
votes
1
reply
381
views
writeVcf save invalid vcf with metadata out of order
variantannotation
updated 3.2 years ago by ★ 6.7k • written 3.2 years ago by ▴ 20
1
vote
7
replies
1.4k
views
Data from ##SAMPLE lines in VCF?
variantannotation coldata
updated 3.3 years ago by ★ 6.7k • written 3.3 years ago by ▴ 10
3
votes
3
replies
592
views
Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
variantannotation
updated 3.6 years ago by ★ 6.7k • written 3.6 years ago by ▴ 10
3
votes
4
replies
714
views
Problem when transforming Platypus vcf to VRanges
variantannotation vcf readvcf vranges
updated 3.6 years ago by 11k • written 3.6 years ago by • 0
0
votes
2
replies
564
views
Error: invalid class "VRanges" object
variantannotation VRanges R Rle
updated 3.6 years ago by ★ 6.7k • written 3.6 years ago by • 0
0
votes
2
replies
625
views
VariantAnnotation::locateVariants error coming from XVector
variantannotation xvector iranges
3.7 years ago Vivek.b ▴ 100
0
votes
2
replies
557
views
filtering a VCF file based on genotype
variantannotation
updated 3.7 years ago by ★ 6.7k • written 3.7 years ago by ▴ 620
0
votes
1
reply
515
views
VariantAnnotation and filtering a VCF
variantannotation
3.7 years ago Bogdan ▴ 620
0
votes
1
reply
528
views
Annotating outdated SNP identifiers
variants variantannotation SNPlocs.Hsapiens.dbSNP150.GRCh38 biomaRt
3.9 years ago sandmann.t ▴ 70
2
votes
2
replies
678
views
[VariantAnnotation] Preserve query metadata with locateVariants()
variantannotation locatevariants metadata mcols
updated 4.1 years ago by ★ 6.7k • written 4.1 years ago by ▴ 590
0
votes
2
replies
2.2k
views
Problem using biocLite() to update packages
biocLite BiocInstaller variantannotation
updated 4.2 years ago by 58k • written 4.2 years ago by ★ 2.0k
0
votes
1
reply
680
views
predictCoding errors with: sequence ^1$ not found
variantannotation predict coding locateVariants granges
4.2 years ago tony j • 0
7
votes
4
replies
1.3k
views
BiocGenerics built with R 3.4.2 changes behaviour
biocgenerics iranges variantannotation
updated 4.3 years ago by 15k • written 4.3 years ago by ▴ 40
7
votes
6
replies
1.0k
views
SNP location annotation problem in "VariantAnnotation" package
annotation variantannotation
updated 4.4 years ago by ★ 6.7k • written 4.4 years ago by ▴ 20
0
votes
4
replies
872
views
Translation Error in predictCoding() for VariantAnnotation
VariantAnnotation
updated 4.4 years ago by 15k • written 4.4 years ago by • 0
8
votes
6
replies
1.2k
views
Error when running "locateVariants" function in "VariantAnnotation" package
variantannotation tidyverse genomicfeatures
updated 4.4 years ago by 15k • written 4.4 years ago by ▴ 20
0
votes
2
replies
906
views
locateVariants function does not find an annotation for the locus
locatevariants txdb.hsapiens.ucsc.hg19.knowngene variantannotation
4.4 years ago Aleksandra • 0
0
votes
1
reply
954
views
Troubleshooting a histogram DataTrack in Gviz
VariantAnnotation gviz
4.5 years ago Russ Fraser ▴ 20
2
votes
5
replies
1.7k
views
VariantAnnotation: Error with ScanVcfParam
variantannotation vcf readvcf filtervcf scanvcfparam
4.5 years ago Didi ▴ 10
0
votes
2
replies
725
views
SNPs in multiple locations
txdb.hsapiens.ucsc.hg19.knowngene ucsc annotation locatevariants variantannotation
updated 4.6 years ago by ★ 6.7k • written 4.6 years ago by • 0
0
votes
1
reply
535
views
summarizeVariants from VariantAnnotation reordering genes in rownames
variantannotation summarizevariants
updated 4.6 years ago by ★ 6.7k • written 4.6 years ago by • 0
3
votes
4
replies
816
views
No annotation for single SNPs
variantannotation SNPs txdb.hsapiens.ucsc.hg19.knowngene ucsc
updated 4.6 years ago by ★ 6.7k • written 4.6 years ago by • 0
0
votes
6
replies
1.3k
views
Error using readVcf
gwastools variantannotation
updated 4.6 years ago by ▴ 820 • written 4.6 years ago by • 0
50 results • Page 1 of 1
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Comment: DiffBind dba.count Error in if (sum(tokeep) < length(tokeep)) by tjhwangxiong • 0
``` https://drive.google.com/drive/folders/1787thVatZpt_KFrfXY-aXV1m0FRm8Mhm?usp=sharing ``` Thanks for your reply. I have uploaded the fil…
Comment: Trying to follow a gene set analyisis in R by Michael Love 35k
No I can’t help with exercises. Just to be clear I’m not affiliated with Harvard and have no supported effort in relation to the edx classe…
Answer: Problems to find the pvalues via rowttests by Gordon Smyth 44k
Ordinary t-tests aren't recommended for genomic analyses because they have poor power and higher false discovery rates. Using the limma p…
Answer: How to insert a qvalues column in a dataframe with pvalues in R by Gordon Smyth 44k
Here and in a previous post, it seems you're not using recommended Bioconductor workflows for Affymetrix microarrays. If you used a standar…
Comment: Trying to follow a gene set analyisis in R by leonardorosas2001 • 0
Thank you. I hope I can still let you know if I have issues with your exercises. They are very challenging but useful! :)
Votes
Answer: Problems to find the pvalues via rowttests
A: How to use subSeq with DNAStringSet and information of GroupedIRanges?
A: How to use subSeq with DNAStringSet and information of GroupedIRanges?
Annotating GRanges with TxDb gene models using plyranges
plyranges select() when a metadata column is shared with core variable
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