Showing : variantAnnotation • reset
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ensemblVEP deprecation and how to reproduce
VariantAnnotation
updated 3 months ago by 6.7k • written 3 months ago by • 0
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377
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Using variantAnnotation to put together genotype and consequence information
variantAnn VariantAnnotation
4 months ago ramiro.barrantes ▴ 10
1
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2
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1.0k
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How to compare subset of samples from VCF files
VCF VariantAnnotation
updated 6 months ago by 52k • written 6 months ago by • 0
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340
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Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
8 months ago Stevie Pederson • 0
0
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1
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428
views
Is random access by row index possible for an indexed VCF file?
Rsamtools VariantAnnotation
updated 9 months ago by 67k • written 9 months ago by ▴ 180
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349
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RFC: significant changes to ensemblVEP package
VariantAnnotation ensemblVEP
11 months ago Vincent J. Carey, Jr. 6.7k
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5
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838
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locateVariant from VariantAnnotation returns wrong results
VariantAnnotation locateVariant
updated 12 months ago by 67k • written 12 months ago by ▴ 70
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849
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Variant Filtering on very large VCF files
VariantAnnotation VariantFiltering
15 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 4.1 years ago by ★ 1.5k
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2
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834
views
Docker usage with Trio Bioconductor Package
VariantAnnotation docker trio
updated 19 months ago by ★ 4.6k • written 19 months ago by • 0
4
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8
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2.1k
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
21 months ago davidhillis • 0
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709
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VariantAnnotation::readVcf incorrectly processes GATK Mutect2 vcf INFO field AS_SB_TABLE
vcf AS_SB_TABLE readVcf Mutect2 VariantAnnotation
22 months ago therealgenna • 0
0
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3
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1.5k
views
Add GP values to VCF
VariantAnnotation
23 months ago Stephanie M. Gogarten ▴ 870
0
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1
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2.0k
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Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123 VariantFiltering Alignment VariantAnnotation
updated 2.1 years ago by 67k • written 2.1 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
2.3 years ago rwan.work • 0
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2
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1.0k
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
2.3 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 11.9 years ago by ▴ 870
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3
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1.3k
views
Problem with intronic variants in VariantAnnotation
VariantAnnotation
updated 2.8 years ago by • 0 • written 3.0 years ago by • 0
0
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2
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1.4k
views
Reading vcf file with readVcf
VariantAnnotation
3.2 years ago aurelien.dejode • 0
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2
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1.0k
views
Multiple exons for predictCoding() from VariantAnnotation (use phase information from gff3 file)?
VariantAnnotation
updated 3.3 years ago by 16k • written 3.4 years ago by • 0
0
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5
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1.7k
views
installation error: Error in setIs(class2, cli, extensionObject = obji, doComplete = FALSE and setClass() for chromVAR and VariantAnnotation
Install VariantAnnotation Bioconductor chromVAR
updated 3.3 years ago by 6.7k • written 3.3 years ago by • 0
0
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1
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1.1k
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GRanges object out-of-bound
VariantAnnotation
updated 3.3 years ago by 6.7k • written 3.4 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 11 months ago by • 0 • written 3.4 years ago by ▴ 470
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0
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747
views
Annotate mutations on DNA level to splice transcripts
VariantAnnotation
3.4 years ago Kasper_holm2 • 0
0
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4
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2.0k
views
Error of read in large vcf file using readVcf
SomaticSignatures VariantAnnotation
updated 3.5 years ago by 67k • written 3.5 years ago by • 0
0
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2
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1.4k
views
VariantAnnotation::readVcf not reading variants
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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2.7k
views
VCF File too large for tabix. Best option to make it usable with R?
samtools tabix VariantAnnotation VCFArray
updated 3.7 years ago by 6.7k • written 3.8 years ago by • 0
1
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12
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3.8k
views
readVcf does not recognize tabix index
VariantAnnotation readvcf tabix
updated 3.7 years ago by 6.7k • written 3.8 years ago by • 0
0
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2
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1.6k
views
readVCF requires the argument "genome". What does it stand for?
Genome readVcf VariantAnnotation
3.8 years ago naive • 0
2
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4
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1.6k
views
Obtaining Comments From VCF Header
VariantAnnotation VCFHeader
written 4.5 years ago by ★ 1.5k
3
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2
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1.6k
views
Import or Subset VCF PASS Variants
VariantAnnotation subset ScanVcfParam
updated 4.7 years ago by 25k • written 4.7 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 4.7 years ago by 25k • written 4.7 years ago by • 0
0
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1
reply
810
views
Can strand be set to minus in VRanges objects?
VariantAnnotation
updated 4.9 years ago by 67k • written 4.9 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 5.2 years ago by 25k • written 5.2 years ago by • 0
2
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3
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1.7k
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 5.4 years ago by ★ 13k • written 5.4 years ago by ▴ 30
2
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3
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1.2k
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VariantAnnotation - subset multi-allele variants
variantAnnotation
updated 5.4 years ago by ★ 11k • written 5.4 years ago by • 0
0
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1
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945
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negative AD value interfering with readVcfasVRanges
VariantAnnotation
updated 5.5 years ago by ★ 11k • written 5.5 years ago by • 0
0
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3
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1.2k
views
rbind VCF Two Objects Column Names Error
VariantAnnotation VCF
5.5 years ago Dario Strbenac ★ 1.5k
0
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0
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929
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predictCoding warning message: serious or not?
software error annotation VariantAnnotation
updated 5.7 years ago by 4.1k • written 5.7 years ago by • 0
2
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3
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1.7k
views
Error in VCF parsing with VariantAnnotation
software error VariantAnnotation ensemblVEP
updated 5.8 years ago by ★ 6.8k • written 5.8 years ago by ▴ 20
4
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9
replies
3.8k
views
Create protein sequences including variants from a VCF file
VariantAnnotation customProDB
updated 7 months ago by • 0 • written 5.8 years ago by ▴ 50
0
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1
reply
1.1k
views
VariantAnnotation fails to load VCF record
variantannotation
6.0 years ago Daniel Cameron ▴ 40
0
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6
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1.8k
views
How to prepare .vcf for seqCAT
seqCAT variantannotation gatk
updated 6.1 years ago by ▴ 30 • written 6.1 years ago by • 0
0
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1
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1.0k
views
writeVcf save invalid vcf with metadata out of order
variantannotation
updated 6.1 years ago by ★ 6.8k • written 6.1 years ago by ▴ 20
1
vote
7
replies
3.6k
views
Data from ##SAMPLE lines in VCF?
variantannotation coldata
updated 6.2 years ago by ★ 6.8k • written 6.2 years ago by ▴ 10
3
votes
3
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1.5k
views
Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
variantannotation
updated 6.5 years ago by ★ 6.8k • written 6.5 years ago by ▴ 10
3
votes
4
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2.0k
views
Problem when transforming Platypus vcf to VRanges
variantannotation vcf readvcf vranges
updated 6.5 years ago by ★ 11k • written 6.5 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 6.5 years ago by ★ 6.8k • written 6.5 years ago by • 0
0
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2
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1.4k
views
VariantAnnotation::locateVariants error coming from XVector
variantannotation xvector iranges
6.6 years ago Vivek.b ▴ 100
0
votes
2
replies
1.9k
views
filtering a VCF file based on genotype
variantannotation
updated 6.6 years ago by ★ 6.8k • written 6.6 years ago by ▴ 670
50 results • Page 1 of 1
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Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by Gordon Smyth 52k
Since the intra-block correlation is negative, it would be best to remove `block` from the model. My experience with genetically identical…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by anna.cot.anna.cot ▴ 30
Thank you! This is actually quite close to my real dataset. I simplified the names to make it easier as an example, but I have now correcte…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Tim Peters ▴ 200
Hi Xiaofei, Is it possible to generate a matrix of beta values or M-values with rownames as probe IDs from this data? If so, cpg.annotate(…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by Gordon Smyth 52k
That looks basically correct, although the terms that you are inputing to `makeContrasts` do not match the condition names in the targets f…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by James W. MacDonald 67k
Oh, right. There's two ways to enter code. If you are in the middle of a sentence and you want to include a function name, you wrap the nam…
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Answer: nightmare to make custom txdb for genomes from ToxoDB
Comment: nightmare to make custom txdb for genomes from ToxoDB
Answer: Normalizing batch effects using technical replicates for DGE analysis between tw
Answer: nightmare to make custom txdb for genomes from ToxoDB
A: Advice on correcting for batch effect using DESeq2
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