Showing : VariantAnnotation • reset
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Problem using locateVariants() from the VariantAnnotation package
VariantAnnotation vari
8 weeks ago • updated 7 weeks ago Marco • 0
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1
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465
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ensemblVEP deprecation and how to reproduce
VariantAnnotation
updated 7 months ago by 6.7k • written 7 months ago by • 0
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512
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Using variantAnnotation to put together genotype and consequence information
variantAnn VariantAnnotation
9 months ago ramiro.barrantes ▴ 10
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2
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1.6k
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How to compare subset of samples from VCF files
VCF VariantAnnotation
updated 10 months ago by 52k • written 10 months ago by • 0
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469
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Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
12 months ago Stevie Pederson • 0
2
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1
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561
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Is random access by row index possible for an indexed VCF file?
Rsamtools VariantAnnotation
updated 13 months ago by 68k • written 13 months ago by ▴ 180
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409
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RFC: significant changes to ensemblVEP package
VariantAnnotation ensemblVEP
15 months ago Vincent J. Carey, Jr. 6.7k
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5
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952
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locateVariant from VariantAnnotation returns wrong results
VariantAnnotation locateVariant
updated 17 months ago by 68k • written 17 months ago by ▴ 70
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1.0k
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Variant Filtering on very large VCF files
VariantAnnotation VariantFiltering
19 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 4.4 years ago by ★ 1.6k
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942
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Docker usage with Trio Bioconductor Package
VariantAnnotation docker trio
updated 23 months ago by ★ 4.8k • written 23 months ago by • 0
4
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8
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2.5k
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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
2.1 years ago davidhillis • 0
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806
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VariantAnnotation::readVcf incorrectly processes GATK Mutect2 vcf INFO field AS_SB_TABLE
vcf AS_SB_TABLE readVcf Mutect2 VariantAnnotation
2.2 years ago therealgenna • 0
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3
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1.8k
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Add GP values to VCF
VariantAnnotation
2.3 years ago Stephanie M. Gogarten ▴ 890
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1
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2.4k
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Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123 VariantFiltering Alignment VariantAnnotation
updated 2.5 years ago by 68k • written 2.5 years ago by ▴ 30
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4
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1.5k
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Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
2.6 years ago rwan.work • 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
2.6 years ago rwan.work • 0
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2
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3.1k
views
merging VCF files
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
written 12.3 years ago by ▴ 890
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3
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1.4k
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Problem with intronic variants in VariantAnnotation
VariantAnnotation
updated 3.1 years ago by • 0 • written 3.3 years ago by • 0
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2
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1.6k
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Reading vcf file with readVcf
VariantAnnotation
3.6 years ago aurelien.dejode • 0
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2
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1.1k
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Multiple exons for predictCoding() from VariantAnnotation (use phase information from gff3 file)?
VariantAnnotation
updated 3.7 years ago by 16k • written 3.8 years ago by • 0
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5
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1.9k
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installation error: Error in setIs(class2, cli, extensionObject = obji, doComplete = FALSE and setClass() for chromVAR and VariantAnnotation
Install VariantAnnotation Bioconductor chromVAR
updated 3.7 years ago by 6.7k • written 3.7 years ago by • 0
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1
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1.2k
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GRanges object out-of-bound
VariantAnnotation
updated 3.7 years ago by 6.7k • written 3.8 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 15 months ago by • 0 • written 3.8 years ago by ▴ 470
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0
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809
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Annotate mutations on DNA level to splice transcripts
VariantAnnotation
3.8 years ago Kasper_holm2 • 0
0
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4
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2.3k
views
Error of read in large vcf file using readVcf
SomaticSignatures 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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1.6k
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VariantAnnotation::readVcf not reading variants
VariantAnnotation
updated 3.9 years ago by 68k • written 3.9 years ago by • 0
0
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2
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3.0k
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VCF File too large for tabix. Best option to make it usable with R?
samtools tabix VariantAnnotation VCFArray
updated 4.1 years ago by 6.7k • written 4.1 years ago by • 0
1
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12
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4.2k
views
readVcf does not recognize tabix index
VariantAnnotation readvcf tabix
updated 4.1 years ago by 6.7k • written 4.1 years ago by • 0
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2
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1.8k
views
readVCF requires the argument "genome". What does it stand for?
Genome readVcf VariantAnnotation
4.1 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 4.8 years ago by ★ 1.6k
3
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2
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1.8k
views
Import or Subset VCF PASS Variants
VariantAnnotation subset ScanVcfParam
updated 5.0 years ago by 25k • written 5.0 years ago by ★ 1.6k
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2
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1.6k
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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
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1
reply
886
views
Can strand be set to minus in VRanges objects?
VariantAnnotation
updated 5.3 years ago by 68k • written 5.3 years ago by • 0
0
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1
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1.6k
views
FilterVCF Filter '' failed: shape of 'skeleton' is not compatible with 'NROW(flesh)'
variantAnnotation
updated 5.5 years ago by 25k • written 5.5 years ago by • 0
2
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3
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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 5.8 years ago by ★ 13k • written 5.8 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 5.8 years ago by ★ 11k • written 5.8 years ago by • 0
0
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1
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1.0k
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negative AD value interfering with readVcfasVRanges
VariantAnnotation
updated 5.8 years ago by ★ 11k • written 5.9 years ago by • 0
0
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3
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1.3k
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rbind VCF Two Objects Column Names Error
VariantAnnotation VCF
5.9 years ago Dario Strbenac ★ 1.6k
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0
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1.0k
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predictCoding warning message: serious or not?
software error annotation VariantAnnotation
updated 6.1 years ago by 4.1k • written 6.1 years ago by • 0
2
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3
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1.9k
views
Error in VCF parsing with VariantAnnotation
software error VariantAnnotation ensemblVEP
updated 6.1 years ago by ★ 6.8k • written 6.1 years ago by ▴ 20
4
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9
replies
4.1k
views
Create protein sequences including variants from a VCF file
VariantAnnotation customProDB
updated 11 months ago by • 0 • written 6.1 years ago by ▴ 50
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1
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1.2k
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VariantAnnotation fails to load VCF record
variantannotation
6.4 years ago Daniel Cameron ▴ 40
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6
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2.0k
views
How to prepare .vcf for seqCAT
seqCAT variantannotation gatk
updated 6.4 years ago by ▴ 30 • written 6.4 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 6.4 years ago by ★ 6.8k • written 6.4 years ago by ▴ 20
1
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7
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3.9k
views
Data from ##SAMPLE lines in VCF?
variantannotation coldata
updated 6.6 years ago by ★ 6.8k • written 6.6 years ago by ▴ 10
3
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3
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1.6k
views
Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
variantannotation
updated 6.8 years ago by ★ 6.8k • written 6.8 years ago by ▴ 10
3
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4
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2.1k
views
Problem when transforming Platypus vcf to VRanges
variantannotation vcf readvcf vranges
updated 6.8 years ago by ★ 11k • written 6.8 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 6.8 years ago by ★ 6.8k • written 6.8 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
6.9 years ago Vivek.b ▴ 100
50 results • Page 1 of 1
Recent ...
Replies
Comment: CluserProfiler message "No gene can be mapped" by Carolina • 0
There is, the overlap that reads out is ( Genes in common: 368 of 368 ). Here is the link for [background genes][1], [term2gene][2], [term2…
Comment: Differing results with DESeq2 by JKim • 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…
Answer: RNA-seq input to GRaNIE by James W. MacDonald 68k
This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…
Answer: Help using reduceSimMatrix with a custom annotation by sergisayolspuig ▴ 80
Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…
Votes
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
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