Showing : variantannotation • reset
0
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2
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136
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Reading vcf file with readVcf
VariantAnnotation
29 days ago • updated 28 days ago aurelien.dejode • 0
0
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2
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181
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Multiple exons for predictCoding() from VariantAnnotation (use phase information from gff3 file)?
VariantAnnotation
updated 7 weeks ago by 15k • written 3 months ago by • 0
0
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5
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232
views
installation error: Error in setIs(class2, cli, extensionObject = obji, doComplete = FALSE and setClass() for chromVAR and VariantAnnotation
Install VariantAnnotation Bioconductor chromVAR
updated 7 weeks ago by 6.5k • written 9 weeks ago by • 0
0
votes
1
reply
101
views
GRanges object out-of-bound
VariantAnnotation
updated 7 weeks ago by 6.5k • written 12 weeks ago by • 0
2
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3
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253
views
readVcf(remoteFile, "hg19", "region") works on macos, fails on linux and in docker
open.BcfFile VariantAnnotation
updated 3 months ago by • 0 • written 3 months ago by ▴ 460
0
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0
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106
views
Annotate mutations on DNA level to splice transcripts
VariantAnnotation
3 months ago Kasper_holm2 • 0
0
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4
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171
views
Error of read in large vcf file using readVcf
SomaticSignatures VariantAnnotation
updated 3 months ago by 58k • written 3 months ago by • 0
0
votes
2
replies
223
views
VariantAnnotation::readVcf not reading variants
VariantAnnotation
updated 5 months ago by 58k • written 5 months ago by • 0
0
votes
2
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362
views
VCF File too large for tabix. Best option to make it usable with R?
samtools tabix VariantAnnotation VCFArray
updated 6 months ago by 6.5k • written 7 months ago by • 0
1
vote
12
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571
views
readVcf does not recognize tabix index
VariantAnnotation readvcf tabix
updated 6 months ago by 6.5k • written 7 months ago by • 0
0
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2
replies
167
views
readVCF requires the argument "genome". What does it stand for?
Genome readVcf VariantAnnotation
7 months ago naive • 0
1
vote
1
reply
229
views
Matching Variants Between Two VCF Objects
VariantAnnotation
updated 10 months ago by ▴ 90 • written 10 months ago by ★ 1.5k
2
votes
2
replies
229
views
Obtaining Comments From VCF Header
VariantAnnotation VCFHeader
updated 15 months ago by 25k • written 15 months ago by ★ 1.5k
3
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2
replies
259
views
Import or Subset VCF PASS Variants
VariantAnnotation subset ScanVcfParam
updated 18 months ago by 25k • written 18 months ago by ★ 1.5k
0
votes
2
replies
206
views
Extract structural variant and flanking sequence from VCF and fasta, in R
VariantAnnotation Bioconductor VCF Structural variants R
updated 18 months ago by 25k • written 18 months ago by • 0
0
votes
1
reply
140
views
Can strand be set to minus in VRanges objects?
VariantAnnotation
updated 21 months ago by 58k • written 21 months ago by • 0
0
votes
1
reply
305
views
FilterVCF Filter '' failed: shape of 'skeleton' is not compatible with 'NROW(flesh)'
variantAnnotation
updated 2.0 years ago by 25k • written 2.0 years ago by • 0
2
votes
3
replies
501
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 2.3 years ago by 13k • written 2.3 years ago by ▴ 30
2
votes
3
replies
255
views
VariantAnnotation - subset multi-allele variants
variantAnnotation
updated 2.3 years ago by 11k • written 2.3 years ago by • 0
0
votes
1
reply
251
views
negative AD value interfering with readVcfasVRanges
VariantAnnotation
updated 2.3 years ago by 11k • written 2.4 years ago by • 0
0
votes
3
replies
374
views
rbind VCF Two Objects Column Names Error
VariantAnnotation VCF
2.4 years ago Dario Strbenac ★ 1.5k
0
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0
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296
views
predictCoding warning message: serious or not?
software error annotation VariantAnnotation
updated 2.6 years ago by 2.8k • written 2.6 years ago by • 0
2
votes
3
replies
461
views
Error in VCF parsing with VariantAnnotation
software error VariantAnnotation ensemblVEP
updated 2.6 years ago by ★ 6.7k • written 2.6 years ago by ▴ 20
3
votes
8
replies
620
views
Create protein sequences including variants from a VCF file
VariantAnnotation customProDB
2.6 years ago daniel.magnus.bader ▴ 40
0
votes
1
reply
407
views
VariantAnnotation fails to load VCF record
variantannotation
2.9 years ago Daniel Cameron ▴ 20
0
votes
6
replies
551
views
How to prepare .vcf for seqCAT
seqCAT variantannotation gatk
updated 2.9 years ago by ▴ 30 • written 2.9 years ago by • 0
0
votes
1
reply
346
views
writeVcf save invalid vcf with metadata out of order
variantannotation
updated 2.9 years ago by ★ 6.7k • written 2.9 years ago by ▴ 20
1
vote
7
replies
1.2k
views
Data from ##SAMPLE lines in VCF?
variantannotation coldata
updated 3.0 years ago by ★ 6.7k • written 3.1 years ago by ▴ 10
3
votes
3
replies
560
views
Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
variantannotation
updated 3.3 years ago by ★ 6.7k • written 3.3 years ago by ▴ 10
3
votes
4
replies
634
views
Problem when transforming Platypus vcf to VRanges
variantannotation vcf readvcf vranges
updated 3.3 years ago by 11k • written 3.3 years ago by • 0
0
votes
2
replies
521
views
Error: invalid class "VRanges" object
variantannotation VRanges R Rle
updated 3.3 years ago by ★ 6.7k • written 3.3 years ago by • 0
0
votes
2
replies
578
views
VariantAnnotation::locateVariants error coming from XVector
variantannotation xvector iranges
3.4 years ago Vivek.b ▴ 100
0
votes
2
replies
512
views
filtering a VCF file based on genotype
variantannotation
updated 3.4 years ago by ★ 6.7k • written 3.4 years ago by ▴ 620
0
votes
1
reply
481
views
VariantAnnotation and filtering a VCF
variantannotation
3.5 years ago Bogdan ▴ 620
0
votes
1
reply
491
views
Annotating outdated SNP identifiers
variants variantannotation SNPlocs.Hsapiens.dbSNP150.GRCh38 biomaRt
3.6 years ago sandmann.t ▴ 70
2
votes
2
replies
642
views
[VariantAnnotation] Preserve query metadata with locateVariants()
variantannotation locatevariants metadata mcols
updated 3.8 years ago by ★ 6.7k • written 3.8 years ago by ▴ 570
0
votes
2
replies
2.1k
views
Problem using biocLite() to update packages
biocLite BiocInstaller variantannotation
updated 3.9 years ago by 58k • written 3.9 years ago by ★ 2.0k
0
votes
1
reply
644
views
predictCoding errors with: sequence ^1$ not found
variantannotation predict coding locateVariants granges
4.0 years ago tony j • 0
7
votes
4
replies
1.2k
views
BiocGenerics built with R 3.4.2 changes behaviour
biocgenerics iranges variantannotation
updated 4.0 years ago by 15k • written 4.1 years ago by ▴ 40
7
votes
6
replies
948
views
SNP location annotation problem in "VariantAnnotation" package
annotation variantannotation
updated 4.1 years ago by ★ 6.7k • written 4.1 years ago by ▴ 20
0
votes
4
replies
833
views
Translation Error in predictCoding() for VariantAnnotation
VariantAnnotation
updated 4.1 years ago by 15k • written 4.1 years ago by • 0
8
votes
6
replies
1.1k
views
Error when running "locateVariants" function in "VariantAnnotation" package
variantannotation tidyverse genomicfeatures
updated 4.1 years ago by 15k • written 4.1 years ago by ▴ 20
0
votes
2
replies
864
views
locateVariants function does not find an annotation for the locus
locatevariants txdb.hsapiens.ucsc.hg19.knowngene variantannotation
4.2 years ago Aleksandra • 0
0
votes
1
reply
913
views
Troubleshooting a histogram DataTrack in Gviz
VariantAnnotation gviz
4.2 years ago Russ Fraser ▴ 20
2
votes
5
replies
1.6k
views
VariantAnnotation: Error with ScanVcfParam
variantannotation vcf readvcf filtervcf scanvcfparam
4.2 years ago Didi ▴ 10
0
votes
2
replies
674
views
SNPs in multiple locations
txdb.hsapiens.ucsc.hg19.knowngene ucsc annotation locatevariants variantannotation
updated 4.3 years ago by ★ 6.7k • written 4.3 years ago by • 0
0
votes
1
reply
508
views
summarizeVariants from VariantAnnotation reordering genes in rownames
variantannotation summarizevariants
updated 4.3 years ago by ★ 6.7k • written 4.3 years ago by • 0
3
votes
4
replies
755
views
No annotation for single SNPs
variantannotation SNPs txdb.hsapiens.ucsc.hg19.knowngene ucsc
updated 4.3 years ago by ★ 6.7k • written 4.3 years ago by • 0
0
votes
6
replies
1.2k
views
Error using readVcf
gwastools variantannotation
updated 4.3 years ago by ▴ 800 • written 4.3 years ago by • 0
3
votes
3
replies
1.4k
views
VariantAnnotation Installation Failure
VariantAnnotation
updated 4.4 years ago by ★ 6.7k • written 4.4 years ago by ▴ 350
50 results • Page 1 of 1
Recent ...
Replies
Comment: how to create an OrgDb package? by Haibo Liu • 0
Thank you so much, James, for the quick response and the fix. I will wait for the release next week. Haibo
Comment: Getting Bioconductor genome wide annotation for Candida auris by James W. MacDonald 58k
If you have C. auris data, then you need to create an `OrgDb`, as I have already noted in my previous answer. The `org.Sc.eg.db` package co…
Comment: window parameter in DataTrack function with a single sample by rbenel ▴ 20
Hi Robert, I think for the most part I figured out some of the issues, but I am still troubled by the yaxis of the `DataTrack` region... …
Comment: R/Bioconductor package for Circulating Cell-Free DNA data analysis by Kevin Blighe 3.4k
Can you elaborate on which type of data you have?, i.e., how have you profiled the cfDNA, and which exact data-type have you now got in you…
Comment: Getting Bioconductor genome wide annotation for Candida auris by Javan Okendo • 0
@James this is the clusterProfiler Rscript I use for enrichment analysis. The data being analyzed is from Candidas auris proteomic data. Th…
Votes
A: topGO and font size in the graph plots
Answer: relationship between bioconda and bioconductor
Comment: Error: package or namespace load failed for ‘clusterProfiler’: object ‘get_fun_f
Comment: Getting Bioconductor genome wide annotation for Candida auris
Answer: Getting Bioconductor genome wide annotation for Candida auris
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