Showing : VariantAnnotation • reset
0
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182
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VariantAnnotation not does escape = within header string quotes
VariantAnnotation
updated 9 weeks ago by ★ 4.0k • written 9 weeks ago by ▴ 40
0
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1
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423
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Problem using locateVariants() from the VariantAnnotation package
VariantAnnotation vari
10 months ago Marco • 0
0
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1
reply
673
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ensemblVEP deprecation and how to reproduce
VariantAnnotation
updated 16 months ago by 6.7k • written 16 months ago by • 0
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0
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710
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Using variantAnnotation to put together genotype and consequence information
variantAnn VariantAnnotation
17 months ago ramiro.barrantes ▴ 10
1
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2
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2.1k
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How to compare subset of samples from VCF files
VCF VariantAnnotation
updated 19 months ago by 53k • written 19 months ago by • 0
0
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0
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622
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Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
21 months ago Stevie Pederson • 0
2
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1
reply
778
views
Is random access by row index possible for an indexed VCF file?
Rsamtools VariantAnnotation
updated 22 months ago by 68k • written 22 months ago by ▴ 180
0
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0
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571
views
RFC: significant changes to ensemblVEP package
VariantAnnotation ensemblVEP
2.0 years ago Vincent J. Carey, Jr. 6.7k
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5
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1.2k
views
locateVariant from VariantAnnotation returns wrong results
VariantAnnotation locateVariant
updated 2.1 years ago by 68k • written 2.1 years ago by ▴ 70
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0
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1.3k
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Variant Filtering on very large VCF files
VariantAnnotation VariantFiltering
2.3 years ago Bogdan ▴ 670
2
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2
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2.2k
views
Matching Variants Between Two VCF Objects
VariantAnnotation
written 5.1 years ago by ★ 1.6k
0
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2
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1.2k
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Docker usage with Trio Bioconductor Package
VariantAnnotation docker trio
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
4
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8
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3.2k
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
2.8 years ago davidhillis • 0
0
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0
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1.0k
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VariantAnnotation::readVcf incorrectly processes GATK Mutect2 vcf INFO field AS_SB_TABLE
vcf AS_SB_TABLE readVcf Mutect2 VariantAnnotation
2.9 years ago therealgenna • 0
0
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3
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2.1k
views
Add GP values to VCF
VariantAnnotation
3.0 years ago Stephanie M. Gogarten ▴ 890
0
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1
reply
3.2k
views
Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123 VariantFiltering Alignment VariantAnnotation
updated 3.2 years ago by 68k • written 3.2 years ago by ▴ 30
2
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4
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1.7k
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
3.3 years ago rwan.work • 0
0
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2
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1.4k
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
3.3 years ago rwan.work • 0
0
votes
2
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3.3k
views
merging VCF files
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
written 13.0 years ago by ▴ 890
0
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3
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1.7k
views
Problem with intronic variants in VariantAnnotation
VariantAnnotation
updated 3.9 years ago by • 0 • written 4.0 years ago by • 0
0
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2
replies
1.9k
views
Reading vcf file with readVcf
VariantAnnotation
4.3 years ago aurelien.dejode • 0
0
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2
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1.3k
views
Multiple exons for predictCoding() from VariantAnnotation (use phase information from gff3 file)?
VariantAnnotation
updated 4.4 years ago by 16k • written 4.5 years ago by • 0
0
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5
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2.2k
views
installation error: Error in setIs(class2, cli, extensionObject = obji, doComplete = FALSE and setClass() for chromVAR and VariantAnnotation
Install VariantAnnotation Bioconductor chromVAR
updated 4.4 years ago by 6.7k • written 4.4 years ago by • 0
0
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1
reply
1.4k
views
GRanges object out-of-bound
VariantAnnotation
updated 4.4 years ago by 6.7k • written 4.5 years ago by • 0
2
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3
replies
1.6k
views
readVcf(remoteFile, "hg19", "region") works on macos, fails on linux and in docker
open.BcfFile VariantAnnotation
updated 24 months ago by • 0 • written 4.5 years ago by ▴ 470
0
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0
replies
924
views
Annotate mutations on DNA level to splice transcripts
VariantAnnotation
4.5 years ago Kasper_holm2 • 0
0
votes
4
replies
2.7k
views
Error of read in large vcf file using readVcf
SomaticSignatures VariantAnnotation
updated 4.5 years ago by 68k • written 4.5 years ago by • 0
0
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2
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1.8k
views
VariantAnnotation::readVcf not reading variants
VariantAnnotation
updated 4.7 years ago by 68k • written 4.7 years ago by • 0
0
votes
2
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3.6k
views
VCF File too large for tabix. Best option to make it usable with R?
samtools tabix VariantAnnotation VCFArray
updated 4.8 years ago by 6.7k • written 4.9 years ago by • 0
1
vote
12
replies
5.0k
views
readVcf does not recognize tabix index
VariantAnnotation readvcf tabix
updated 4.8 years ago by 6.7k • written 4.8 years ago by • 0
0
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2
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2.2k
views
readVCF requires the argument "genome". What does it stand for?
Genome readVcf VariantAnnotation
4.8 years ago naive • 0
2
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4
replies
2.2k
views
Obtaining Comments From VCF Header
VariantAnnotation VCFHeader
written 5.5 years ago by ★ 1.6k
3
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2
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2.0k
views
Import or Subset VCF PASS Variants
VariantAnnotation subset ScanVcfParam
updated 5.7 years ago by 25k • written 5.7 years ago by ★ 1.6k
0
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2
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1.9k
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Extract structural variant and flanking sequence from VCF and fasta, in R
VariantAnnotation Bioconductor VCF Structural variants R
updated 5.8 years ago by 25k • written 5.8 years ago by • 0
0
votes
1
reply
1.0k
views
Can strand be set to minus in VRanges objects?
VariantAnnotation
updated 6.0 years ago by 68k • written 6.0 years ago by • 0
0
votes
1
reply
1.8k
views
FilterVCF Filter '' failed: shape of 'skeleton' is not compatible with 'NROW(flesh)'
variantAnnotation
updated 6.3 years ago by 25k • written 6.3 years ago by • 0
2
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3
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2.3k
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 6.5 years ago by ★ 13k • written 6.5 years ago by ▴ 30
2
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3
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1.7k
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VariantAnnotation - subset multi-allele variants
variantAnnotation
updated 6.5 years ago by ★ 11k • written 6.5 years ago by • 0
0
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1
reply
1.2k
views
negative AD value interfering with readVcfasVRanges
VariantAnnotation
updated 6.6 years ago by ★ 11k • written 6.6 years ago by • 0
0
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3
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1.5k
views
rbind VCF Two Objects Column Names Error
VariantAnnotation VCF
6.6 years ago Dario Strbenac ★ 1.6k
0
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0
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1.2k
views
predictCoding warning message: serious or not?
software error annotation VariantAnnotation
updated 6.8 years ago by 4.3k • written 6.8 years ago by • 0
2
votes
3
replies
2.2k
views
Error in VCF parsing with VariantAnnotation
software error VariantAnnotation ensemblVEP
updated 6.8 years ago by ★ 6.8k • written 6.8 years ago by ▴ 20
4
votes
9
replies
4.7k
views
Create protein sequences including variants from a VCF file
VariantAnnotation customProDB
updated 20 months ago by • 0 • written 6.9 years ago by ▴ 50
0
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1
reply
1.3k
views
VariantAnnotation fails to load VCF record
variantannotation
7.1 years ago Daniel Cameron ▴ 40
0
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6
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2.3k
views
How to prepare .vcf for seqCAT
seqCAT variantannotation gatk
updated 7.1 years ago by ▴ 30 • written 7.1 years ago by • 0
0
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1
reply
1.3k
views
writeVcf save invalid vcf with metadata out of order
variantannotation
updated 7.2 years ago by ★ 6.8k • written 7.2 years ago by ▴ 20
1
vote
7
replies
4.5k
views
Data from ##SAMPLE lines in VCF?
variantannotation coldata
updated 7.3 years ago by ★ 6.8k • written 7.3 years ago by ▴ 10
3
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3
replies
1.9k
views
Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
variantannotation
updated 7.5 years ago by ★ 6.8k • written 7.5 years ago by ▴ 10
3
votes
4
replies
2.4k
views
Problem when transforming Platypus vcf to VRanges
variantannotation vcf readvcf vranges
updated 7.5 years ago by ★ 11k • written 7.5 years ago by • 0
0
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2
replies
1.7k
views
Error: invalid class "VRanges" object
variantannotation VRanges R Rle
updated 7.6 years ago by ★ 6.8k • written 7.6 years ago by • 0
217 results • Page 1 of 5
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Replies
Answer: Confounded design, batch effect correction (edgeR) by nig.httopss • 0
To perform gene matching accurately, you should use the formula ~0 + Group + Batch in the design matrix to better manage sample groups. Sin…
Comment: Clarification on counting in Rsubread (featureCounts) by Gordon Smyth 53k
Have you told featureCounts to do strand-specific counting? As pointed out by Frances Turner, you can lose reads if they overlap the gene …
Answer: Clarification on counting in Rsubread (featureCounts) by Frances Turner ▴ 10
You should look at the summary files produced by feature counts. This gives a breakdown of what happened to reads that were not assigned. Y…
Comment: Incosistencies in buildSNNGraph() function by ATpoint ★ 5.0k
Just played with this a bit and I think it comes down to not having a fixed seed before running the leiden thingy. Same goes for PCA and UM…
Answer: Incosistencies in buildSNNGraph() function by Aaron Lun ★ 29k
The most obvious thing that comes to mind is the RNG seed. `cluster_leiden()` does some random number generation, somewhere deep in the **i…
Votes
Answer: Clarification on counting in Rsubread (featureCounts)
C: RNA-Seq analysis with Limma/edgeR, time course experiment, aberrant results
C: RNA-Seq analysis with Limma/edgeR, time course experiment, aberrant results
A: Conversion from counts to FPKM
Answer: Incosistencies in buildSNNGraph() function
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