Showing : variantannotation • reset
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306
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Problem using locateVariants() from the VariantAnnotation package
VariantAnnotation vari
4 months ago Marco • 0
0
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1
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528
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ensemblVEP deprecation and how to reproduce
VariantAnnotation
updated 10 months ago by 6.7k • written 10 months ago by • 0
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573
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Using variantAnnotation to put together genotype and consequence information
variantAnn VariantAnnotation
11 months ago ramiro.barrantes ▴ 10
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2
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1.8k
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How to compare subset of samples from VCF files
VCF VariantAnnotation
updated 13 months ago by 52k • written 13 months ago by • 0
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512
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Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
15 months ago Stevie Pederson • 0
2
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1
reply
618
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Is random access by row index possible for an indexed VCF file?
Rsamtools VariantAnnotation
updated 16 months ago by 68k • written 16 months ago by ▴ 180
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0
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455
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RFC: significant changes to ensemblVEP package
VariantAnnotation ensemblVEP
18 months ago Vincent J. Carey, Jr. 6.7k
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5
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1.0k
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locateVariant from VariantAnnotation returns wrong results
VariantAnnotation locateVariant
updated 19 months ago by 68k • written 19 months ago by ▴ 70
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1.1k
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Variant Filtering on very large VCF files
VariantAnnotation VariantFiltering
21 months ago Bogdan ▴ 670
2
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2
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1.9k
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Matching Variants Between Two VCF Objects
VariantAnnotation
written 4.6 years ago by ★ 1.6k
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2
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1.0k
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Docker usage with Trio Bioconductor Package
VariantAnnotation docker trio
updated 2.2 years ago by ★ 4.9k • written 2.2 years ago by • 0
4
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8
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2.6k
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
2.3 years ago davidhillis • 0
0
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0
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872
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VariantAnnotation::readVcf incorrectly processes GATK Mutect2 vcf INFO field AS_SB_TABLE
vcf AS_SB_TABLE readVcf Mutect2 VariantAnnotation
2.4 years ago therealgenna • 0
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3
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1.8k
views
Add GP values to VCF
VariantAnnotation
2.5 years ago Stephanie M. Gogarten ▴ 890
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1
reply
2.6k
views
Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123 VariantFiltering Alignment VariantAnnotation
updated 2.7 years ago by 68k • written 2.7 years ago by ▴ 30
2
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4
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1.5k
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
2.8 years ago rwan.work • 0
0
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2
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1.2k
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Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
2.8 years ago rwan.work • 0
0
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2
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3.1k
views
merging VCF files
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
written 12.5 years ago by ▴ 890
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3
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1.5k
views
Problem with intronic variants in VariantAnnotation
VariantAnnotation
updated 3.4 years ago by • 0 • written 3.5 years ago by • 0
0
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2
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1.7k
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Reading vcf file with readVcf
VariantAnnotation
3.8 years ago aurelien.dejode • 0
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2
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1.2k
views
Multiple exons for predictCoding() from VariantAnnotation (use phase information from gff3 file)?
VariantAnnotation
updated 3.9 years ago by 16k • written 4.0 years ago by • 0
0
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5
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2.0k
views
installation error: Error in setIs(class2, cli, extensionObject = obji, doComplete = FALSE and setClass() for chromVAR and VariantAnnotation
Install VariantAnnotation Bioconductor chromVAR
updated 3.9 years ago by 6.7k • written 3.9 years ago by • 0
0
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1
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1.3k
views
GRanges object out-of-bound
VariantAnnotation
updated 3.9 years ago by 6.7k • written 4.0 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 17 months ago by • 0 • written 4.0 years ago by ▴ 470
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0
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837
views
Annotate mutations on DNA level to splice transcripts
VariantAnnotation
4.0 years ago Kasper_holm2 • 0
0
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4
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2.5k
views
Error of read in large vcf file using readVcf
SomaticSignatures VariantAnnotation
updated 4.0 years ago by 68k • written 4.0 years ago by • 0
0
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2
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1.6k
views
VariantAnnotation::readVcf not reading variants
VariantAnnotation
updated 4.1 years ago by 68k • written 4.1 years ago by • 0
0
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2
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3.2k
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VCF File too large for tabix. Best option to make it usable with R?
samtools tabix VariantAnnotation VCFArray
updated 4.3 years ago by 6.7k • written 4.4 years ago by • 0
1
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12
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4.5k
views
readVcf does not recognize tabix index
VariantAnnotation readvcf tabix
updated 4.3 years ago by 6.7k • written 4.3 years ago by • 0
0
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2
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1.9k
views
readVCF requires the argument "genome". What does it stand for?
Genome readVcf VariantAnnotation
4.3 years ago naive • 0
2
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4
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1.9k
views
Obtaining Comments From VCF Header
VariantAnnotation VCFHeader
written 5.0 years ago by ★ 1.6k
3
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2
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1.9k
views
Import or Subset VCF PASS Variants
VariantAnnotation subset ScanVcfParam
updated 5.2 years ago by 25k • written 5.2 years ago by ★ 1.6k
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2
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1.7k
views
Extract structural variant and flanking sequence from VCF and fasta, in R
VariantAnnotation Bioconductor VCF Structural variants R
updated 5.3 years ago by 25k • written 5.3 years ago by • 0
0
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1
reply
922
views
Can strand be set to minus in VRanges objects?
VariantAnnotation
updated 5.5 years ago by 68k • written 5.5 years ago by • 0
0
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1
reply
1.7k
views
FilterVCF Filter '' failed: shape of 'skeleton' is not compatible with 'NROW(flesh)'
variantAnnotation
updated 5.8 years ago by 25k • written 5.8 years ago by • 0
2
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3
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2.0k
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 6.0 years ago by ★ 13k • written 6.0 years ago by ▴ 30
2
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3
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1.4k
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VariantAnnotation - subset multi-allele variants
variantAnnotation
updated 6.0 years ago by ★ 11k • written 6.0 years ago by • 0
0
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1
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1.1k
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negative AD value interfering with readVcfasVRanges
VariantAnnotation
updated 6.1 years ago by ★ 11k • written 6.1 years ago by • 0
0
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3
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1.4k
views
rbind VCF Two Objects Column Names Error
VariantAnnotation VCF
6.1 years ago Dario Strbenac ★ 1.6k
0
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0
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1.1k
views
predictCoding warning message: serious or not?
software error annotation VariantAnnotation
updated 6.3 years ago by 4.2k • written 6.3 years ago by • 0
2
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3
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2.0k
views
Error in VCF parsing with VariantAnnotation
software error VariantAnnotation ensemblVEP
updated 6.3 years ago by ★ 6.8k • written 6.3 years ago by ▴ 20
4
votes
9
replies
4.3k
views
Create protein sequences including variants from a VCF file
VariantAnnotation customProDB
updated 14 months ago by • 0 • written 6.4 years ago by ▴ 50
0
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1
reply
1.2k
views
VariantAnnotation fails to load VCF record
variantannotation
6.6 years ago Daniel Cameron ▴ 40
0
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6
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2.1k
views
How to prepare .vcf for seqCAT
seqCAT variantannotation gatk
updated 6.6 years ago by ▴ 30 • written 6.6 years ago by • 0
0
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1
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1.1k
views
writeVcf save invalid vcf with metadata out of order
variantannotation
updated 6.6 years ago by ★ 6.8k • written 6.7 years ago by ▴ 20
1
vote
7
replies
4.1k
views
Data from ##SAMPLE lines in VCF?
variantannotation coldata
updated 6.8 years ago by ★ 6.8k • written 6.8 years ago by ▴ 10
3
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3
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1.7k
views
Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
variantannotation
updated 7.0 years ago by ★ 6.8k • written 7.0 years ago by ▴ 10
3
votes
4
replies
2.2k
views
Problem when transforming Platypus vcf to VRanges
variantannotation vcf readvcf vranges
updated 7.0 years ago by ★ 11k • written 7.0 years ago by • 0
0
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2
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1.5k
views
Error: invalid class "VRanges" object
variantannotation VRanges R Rle
updated 7.0 years ago by ★ 6.8k • written 7.0 years ago by • 0
0
votes
2
replies
1.6k
views
VariantAnnotation::locateVariants error coming from XVector
variantannotation xvector iranges
7.1 years ago Vivek.b ▴ 100
50 results • Page 1 of 1
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Answer: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by Aaron Lun ★ 28k
Consider using a `SVT_SparseMatrix` from the **SparseArray** package, which is explicitly designed for this. **DropletUtils** (in BioC-deve…
Comment: Regarding the issue of background genes in enrichment analysis by zalinkaelisa • 0
Use good features to distinguish the situation of the type of experiment [baseball 9][1] [1]: https://baseball9.io/
Comment: Heatmap of the Count Matrix by gta5movilecom • 0
Using it for the top 20 genes in the heatmap highlights high-expression genes, but may miss out on variance-driven patterns. If you want to…
Answer: Regarding the issue of background genes in enrichment analysis by ATpoint ★ 4.9k
It should imo be the genes that were eligable to yield a "significant" result in your analysis. So, if you test set is derived from differe…
Comment: Applying lmFit(), eBayes() and topTable() for modeling associations between NMR- by Gordon Smyth 52k
> How do these logFC values compare to standard effect sizes derived using a basic regression model like lm()? Exactly the same. Both soft…
Votes
Regarding the issue of background genes in enrichment analysis
Best practice for handling large data (matrix with >2^31-1 non-zero elements) in SingleCellExperiment?
Comment: How can I avoid artifacts in gene set/pathway scoring by UCell and similar algor
Answer: I would like to perform differential expression analysis of lncRNAs using DESeq2
I would like to perform differential expression analysis of lncRNAs using DESeq2 and edgeR.
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