Showing : VariantAnnotation • reset
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174
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Problem using locateVariants() from the VariantAnnotation package
VariantAnnotation vari
20 days ago • updated 19 days ago Marco • 0
0
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1
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415
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ensemblVEP deprecation and how to reproduce
VariantAnnotation
updated 6 months ago by 6.7k • written 6 months ago by • 0
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0
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468
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Using variantAnnotation to put together genotype and consequence information
variantAnn VariantAnnotation
8 months ago ramiro.barrantes ▴ 10
1
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2
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1.5k
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How to compare subset of samples from VCF files
VCF VariantAnnotation
updated 9 months ago by 52k • written 9 months ago by • 0
0
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0
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439
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Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
11 months ago Stevie Pederson • 0
0
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1
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495
views
Is random access by row index possible for an indexed VCF file?
Rsamtools VariantAnnotation
updated 12 months ago by 68k • written 12 months ago by ▴ 180
0
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0
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393
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RFC: significant changes to ensemblVEP package
VariantAnnotation ensemblVEP
14 months ago Vincent J. Carey, Jr. 6.7k
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5
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918
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locateVariant from VariantAnnotation returns wrong results
VariantAnnotation locateVariant
updated 15 months ago by 68k • written 15 months ago by ▴ 70
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974
views
Variant Filtering on very large VCF files
VariantAnnotation VariantFiltering
18 months ago Bogdan ▴ 670
2
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2
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1.9k
views
Matching Variants Between Two VCF Objects
VariantAnnotation
written 4.3 years ago by ★ 1.6k
0
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2
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909
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Docker usage with Trio Bioconductor Package
VariantAnnotation docker trio
updated 22 months ago by ★ 4.7k • written 22 months ago by • 0
4
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8
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2.4k
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
2.0 years ago davidhillis • 0
0
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0
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779
views
VariantAnnotation::readVcf incorrectly processes GATK Mutect2 vcf INFO field AS_SB_TABLE
vcf AS_SB_TABLE readVcf Mutect2 VariantAnnotation
2.1 years ago therealgenna • 0
0
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3
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1.7k
views
Add GP values to VCF
VariantAnnotation
2.2 years ago Stephanie M. Gogarten ▴ 890
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1
reply
2.3k
views
Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123 VariantFiltering Alignment VariantAnnotation
updated 2.4 years ago by 68k • written 2.4 years ago by ▴ 30
2
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4
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1.4k
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
2.5 years ago rwan.work • 0
0
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2
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1.1k
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
2.5 years ago rwan.work • 0
0
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2
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3.0k
views
merging VCF files
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
written 12.2 years ago by ▴ 890
0
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3
replies
1.3k
views
Problem with intronic variants in VariantAnnotation
VariantAnnotation
updated 3.0 years ago by • 0 • written 3.2 years ago by • 0
0
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2
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1.6k
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Reading vcf file with readVcf
VariantAnnotation
3.5 years ago aurelien.dejode • 0
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2
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1.1k
views
Multiple exons for predictCoding() from VariantAnnotation (use phase information from gff3 file)?
VariantAnnotation
updated 3.6 years ago by 16k • written 3.7 years ago by • 0
0
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5
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1.8k
views
installation error: Error in setIs(class2, cli, extensionObject = obji, doComplete = FALSE and setClass() for chromVAR and VariantAnnotation
Install VariantAnnotation Bioconductor chromVAR
updated 3.6 years ago by 6.7k • written 3.6 years ago by • 0
0
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1
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1.2k
views
GRanges object out-of-bound
VariantAnnotation
updated 3.6 years ago by 6.7k • written 3.7 years ago by • 0
2
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3
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1.4k
views
readVcf(remoteFile, "hg19", "region") works on macos, fails on linux and in docker
open.BcfFile VariantAnnotation
updated 14 months ago by • 0 • written 3.7 years ago by ▴ 470
0
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0
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798
views
Annotate mutations on DNA level to splice transcripts
VariantAnnotation
3.7 years ago Kasper_holm2 • 0
0
votes
4
replies
2.2k
views
Error of read in large vcf file using readVcf
SomaticSignatures VariantAnnotation
updated 3.7 years ago by 68k • written 3.7 years ago by • 0
0
votes
2
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1.5k
views
VariantAnnotation::readVcf not reading variants
VariantAnnotation
updated 3.8 years ago by 68k • written 3.8 years ago by • 0
0
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2
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2.9k
views
VCF File too large for tabix. Best option to make it usable with R?
samtools tabix VariantAnnotation VCFArray
updated 4.0 years ago by 6.7k • written 4.0 years ago by • 0
1
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12
replies
4.1k
views
readVcf does not recognize tabix index
VariantAnnotation readvcf tabix
updated 4.0 years ago by 6.7k • written 4.0 years ago by • 0
0
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2
replies
1.8k
views
readVCF requires the argument "genome". What does it stand for?
Genome readVcf VariantAnnotation
4.0 years ago naive • 0
2
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4
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1.8k
views
Obtaining Comments From VCF Header
VariantAnnotation VCFHeader
written 4.7 years ago by ★ 1.6k
3
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2
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1.7k
views
Import or Subset VCF PASS Variants
VariantAnnotation subset ScanVcfParam
updated 4.9 years ago by 25k • written 4.9 years ago by ★ 1.6k
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2
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1.5k
views
Extract structural variant and flanking sequence from VCF and fasta, in R
VariantAnnotation Bioconductor VCF Structural variants R
updated 5.0 years ago by 25k • written 5.0 years ago by • 0
0
votes
1
reply
868
views
Can strand be set to minus in VRanges objects?
VariantAnnotation
updated 5.2 years ago by 68k • written 5.2 years ago by • 0
0
votes
1
reply
1.6k
views
FilterVCF Filter '' failed: shape of 'skeleton' is not compatible with 'NROW(flesh)'
variantAnnotation
updated 5.4 years ago by 25k • written 5.4 years ago by • 0
2
votes
3
replies
1.9k
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 5.7 years ago by ★ 13k • written 5.7 years ago by ▴ 30
2
votes
3
replies
1.3k
views
VariantAnnotation - subset multi-allele variants
variantAnnotation
updated 5.7 years ago by ★ 11k • written 5.7 years ago by • 0
0
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1
reply
1.0k
views
negative AD value interfering with readVcfasVRanges
VariantAnnotation
updated 5.8 years ago by ★ 11k • written 5.8 years ago by • 0
0
votes
3
replies
1.3k
views
rbind VCF Two Objects Column Names Error
VariantAnnotation VCF
5.8 years ago Dario Strbenac ★ 1.6k
0
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0
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994
views
predictCoding warning message: serious or not?
software error annotation VariantAnnotation
updated 6.0 years ago by 4.1k • written 6.0 years ago by • 0
2
votes
3
replies
1.9k
views
Error in VCF parsing with VariantAnnotation
software error VariantAnnotation ensemblVEP
updated 6.0 years ago by ★ 6.8k • written 6.0 years ago by ▴ 20
4
votes
9
replies
4.0k
views
Create protein sequences including variants from a VCF file
VariantAnnotation customProDB
updated 10 months ago by • 0 • written 6.0 years ago by ▴ 50
0
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1
reply
1.2k
views
VariantAnnotation fails to load VCF record
variantannotation
6.3 years ago Daniel Cameron ▴ 40
0
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6
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2.0k
views
How to prepare .vcf for seqCAT
seqCAT variantannotation gatk
updated 6.3 years ago by ▴ 30 • written 6.3 years ago by • 0
0
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1
reply
1.1k
views
writeVcf save invalid vcf with metadata out of order
variantannotation
updated 6.3 years ago by ★ 6.8k • written 6.3 years ago by ▴ 20
1
vote
7
replies
3.8k
views
Data from ##SAMPLE lines in VCF?
variantannotation coldata
updated 6.5 years ago by ★ 6.8k • written 6.5 years ago by ▴ 10
3
votes
3
replies
1.6k
views
Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
variantannotation
updated 6.7 years ago by ★ 6.8k • written 6.7 years ago by ▴ 10
3
votes
4
replies
2.1k
views
Problem when transforming Platypus vcf to VRanges
variantannotation vcf readvcf vranges
updated 6.7 years ago by ★ 11k • written 6.7 years ago by • 0
0
votes
2
replies
1.5k
views
Error: invalid class "VRanges" object
variantannotation VRanges R Rle
updated 6.7 years ago by ★ 6.8k • written 6.7 years ago by • 0
0
votes
2
replies
1.5k
views
VariantAnnotation::locateVariants error coming from XVector
variantannotation xvector iranges
6.8 years ago Vivek.b ▴ 100
50 results • Page 1 of 1
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Comment: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with by Gordon Smyth 52k
I generally recommend `block=individual` for unbalanced designs, to recover information from incomplete blocks. I would only be disuaded fr…
Comment: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with by Devin ▴ 10
Thank you, Gordon, for your responses to all of my questions. For analysis A), in the case when a patient has either a missing timepoint or…
Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0
Thanks Michael. Just out of curiosity, would you also use the same technique for things like clustering analysis or when looking at the abn…
Comment: GAGE kegg.gsets() self-signed certificate error by Lucas • 0
Hello, I ended up solving the issue by using the first strategy: Disable the SSL certificate Verification. I used the following code to …
Comment: Clarification on GOALL / GO2ALLORFs mapping by DavideSant • 0
Thank you for your answer James. I have to disagree though, at the SGD webpage you posted there is no indication that "GO:0045719 - negati…
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Comment: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
Answer: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
Answer: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
Answer: Using TPM from tximport of Salmon output for singscore
Comment: Using TPM from tximport of Salmon output for singscore
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