Showing : VariantAnnotation • reset
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ensemblVEP deprecation and how to reproduce
VariantAnnotation
updated 4 months ago by 6.7k • written 4 months ago by • 0
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406
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Using variantAnnotation to put together genotype and consequence information
variantAnn VariantAnnotation
6 months ago ramiro.barrantes ▴ 10
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2
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1.2k
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How to compare subset of samples from VCF files
VCF VariantAnnotation
updated 7 months ago by 52k • written 8 months ago by • 0
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370
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Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
9 months ago Stevie Pederson • 0
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1
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453
views
Is random access by row index possible for an indexed VCF file?
Rsamtools VariantAnnotation
updated 10 months ago by 67k • written 10 months ago by ▴ 180
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364
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RFC: significant changes to ensemblVEP package
VariantAnnotation ensemblVEP
12 months ago Vincent J. Carey, Jr. 6.7k
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5
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870
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locateVariant from VariantAnnotation returns wrong results
VariantAnnotation locateVariant
updated 14 months ago by 67k • written 14 months ago by ▴ 70
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895
views
Variant Filtering on very large VCF files
VariantAnnotation VariantFiltering
16 months ago Bogdan ▴ 670
2
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2
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1.8k
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Matching Variants Between Two VCF Objects
VariantAnnotation
written 4.2 years ago by ★ 1.5k
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2
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862
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Docker usage with Trio Bioconductor Package
VariantAnnotation docker trio
updated 20 months ago by ★ 4.6k • written 20 months ago by • 0
4
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8
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2.2k
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
22 months ago davidhillis • 0
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734
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VariantAnnotation::readVcf incorrectly processes GATK Mutect2 vcf INFO field AS_SB_TABLE
vcf AS_SB_TABLE readVcf Mutect2 VariantAnnotation
23 months ago therealgenna • 0
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3
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1.6k
views
Add GP values to VCF
VariantAnnotation
2.1 years ago • updated 2.0 years ago Stephanie M. Gogarten ▴ 890
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1
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2.1k
views
Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123 VariantFiltering Alignment VariantAnnotation
updated 2.2 years ago by 67k • written 2.2 years ago by ▴ 30
2
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4
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1.3k
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
2.4 years ago rwan.work • 0
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2
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1.1k
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
2.4 years ago rwan.work • 0
0
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2
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2.9k
views
merging VCF files
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
written 12.1 years ago by ▴ 890
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3
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1.3k
views
Problem with intronic variants in VariantAnnotation
VariantAnnotation
updated 2.9 years ago by • 0 • written 3.1 years ago by • 0
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2
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1.5k
views
Reading vcf file with readVcf
VariantAnnotation
3.4 years ago aurelien.dejode • 0
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2
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1.0k
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Multiple exons for predictCoding() from VariantAnnotation (use phase information from gff3 file)?
VariantAnnotation
updated 3.4 years ago by 16k • written 3.5 years ago by • 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 3.4 years ago by 6.7k • written 3.5 years ago by • 0
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1
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1.1k
views
GRanges object out-of-bound
VariantAnnotation
updated 3.4 years ago by 6.7k • written 3.5 years ago by • 0
2
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3
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1.3k
views
readVcf(remoteFile, "hg19", "region") works on macos, fails on linux and in docker
open.BcfFile VariantAnnotation
updated 12 months ago by • 0 • written 3.6 years ago by ▴ 470
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0
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773
views
Annotate mutations on DNA level to splice transcripts
VariantAnnotation
3.5 years ago Kasper_holm2 • 0
0
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4
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2.1k
views
Error of read in large vcf file using readVcf
SomaticSignatures VariantAnnotation
updated 3.6 years ago by 67k • written 3.6 years ago by • 0
0
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2
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1.5k
views
VariantAnnotation::readVcf not reading variants
VariantAnnotation
updated 3.7 years ago by 67k • written 3.7 years ago by • 0
0
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2
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2.8k
views
VCF File too large for tabix. Best option to make it usable with R?
samtools tabix VariantAnnotation VCFArray
updated 3.8 years ago by 6.7k • written 3.9 years ago by • 0
1
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12
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3.9k
views
readVcf does not recognize tabix index
VariantAnnotation readvcf tabix
updated 3.8 years ago by 6.7k • written 3.9 years ago by • 0
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2
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1.7k
views
readVCF requires the argument "genome". What does it stand for?
Genome readVcf VariantAnnotation
3.9 years ago naive • 0
2
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4
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1.7k
views
Obtaining Comments From VCF Header
VariantAnnotation VCFHeader
written 4.6 years ago by ★ 1.5k
3
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2
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1.7k
views
Import or Subset VCF PASS Variants
VariantAnnotation subset ScanVcfParam
updated 4.8 years ago by 25k • written 4.8 years ago by ★ 1.5k
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2
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1.4k
views
Extract structural variant and flanking sequence from VCF and fasta, in R
VariantAnnotation Bioconductor VCF Structural variants R
updated 4.8 years ago by 25k • written 4.8 years ago by • 0
0
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1
reply
827
views
Can strand be set to minus in VRanges objects?
VariantAnnotation
updated 5.0 years ago by 67k • written 5.0 years ago by • 0
0
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1
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1.5k
views
FilterVCF Filter '' failed: shape of 'skeleton' is not compatible with 'NROW(flesh)'
variantAnnotation
updated 5.3 years ago by 25k • written 5.3 years ago by • 0
2
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3
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1.8k
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 5.5 years ago by ★ 13k • written 5.5 years ago by ▴ 30
2
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3
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1.3k
views
VariantAnnotation - subset multi-allele variants
variantAnnotation
updated 5.6 years ago by ★ 11k • written 5.6 years ago by • 0
0
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1
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975
views
negative AD value interfering with readVcfasVRanges
VariantAnnotation
updated 5.6 years ago by ★ 11k • written 5.6 years ago by • 0
0
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3
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1.3k
views
rbind VCF Two Objects Column Names Error
VariantAnnotation VCF
5.7 years ago Dario Strbenac ★ 1.5k
0
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0
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950
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predictCoding warning message: serious or not?
software error annotation VariantAnnotation
updated 5.8 years ago by 4.1k • written 5.8 years ago by • 0
2
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3
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1.8k
views
Error in VCF parsing with VariantAnnotation
software error VariantAnnotation ensemblVEP
updated 5.9 years ago by ★ 6.8k • written 5.9 years ago by ▴ 20
4
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9
replies
3.9k
views
Create protein sequences including variants from a VCF file
VariantAnnotation customProDB
updated 8 months ago by • 0 • written 5.9 years ago by ▴ 50
0
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1
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1.1k
views
VariantAnnotation fails to load VCF record
variantannotation
6.1 years ago Daniel Cameron ▴ 40
0
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6
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1.9k
views
How to prepare .vcf for seqCAT
seqCAT variantannotation gatk
updated 6.2 years ago by ▴ 30 • written 6.2 years ago by • 0
0
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1
reply
1.0k
views
writeVcf save invalid vcf with metadata out of order
variantannotation
updated 6.2 years ago by ★ 6.8k • written 6.2 years ago by ▴ 20
1
vote
7
replies
3.7k
views
Data from ##SAMPLE lines in VCF?
variantannotation coldata
updated 6.3 years ago by ★ 6.8k • written 6.3 years ago by ▴ 10
3
votes
3
replies
1.5k
views
Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
variantannotation
updated 6.6 years ago by ★ 6.8k • written 6.6 years ago by ▴ 10
3
votes
4
replies
2.0k
views
Problem when transforming Platypus vcf to VRanges
variantannotation vcf readvcf vranges
updated 6.6 years ago by ★ 11k • written 6.6 years ago by • 0
0
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2
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1.4k
views
Error: invalid class "VRanges" object
variantannotation VRanges R Rle
updated 6.6 years ago by ★ 6.8k • written 6.6 years ago by • 0
0
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2
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1.5k
views
VariantAnnotation::locateVariants error coming from XVector
variantannotation xvector iranges
6.7 years ago Vivek.b ▴ 100
0
votes
2
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2.0k
views
filtering a VCF file based on genotype
variantannotation
updated 6.7 years ago by ★ 6.8k • written 6.7 years ago by ▴ 670
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Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
I see. Thank you ATpoint!
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Prakash Sah • 0
Thanks James!
Comment: Why select top highly expressed genes based on normalized counts, but then plot by ATpoint ★ 4.6k
I think I explained what the differences between approach 1 and 2 is in my answer. I assume that the tutorial uses vst because it is varian…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
Thank you ATpoint for your responses. I am a bit confused because the difference between the two approaches is the selection of the genes…
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Comment: can't install tscR
Answer: Csaw normalization strategies - general inquiry
A: DESeq2 interaction term
Comment: Recount3 data correspond to TCGA data
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