Showing : variantAnnotation • reset
0
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158
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VariantAnnotation not does escape = within header string quotes
VariantAnnotation
updated 5 weeks ago by ★ 4.0k • written 5 weeks ago by ▴ 40
0
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1
reply
391
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Problem using locateVariants() from the VariantAnnotation package
VariantAnnotation vari
9 months ago Marco • 0
0
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1
reply
628
views
ensemblVEP deprecation and how to reproduce
VariantAnnotation
updated 15 months ago by 6.7k • written 15 months ago by • 0
0
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0
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667
views
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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2.0k
views
How to compare subset of samples from VCF files
VCF VariantAnnotation
updated 18 months ago by 53k • written 18 months ago by • 0
0
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0
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604
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
20 months ago Stevie Pederson • 0
2
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1
reply
755
views
Is random access by row index possible for an indexed VCF file?
Rsamtools VariantAnnotation
updated 21 months ago by 68k • written 21 months ago by ▴ 180
0
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0
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549
views
RFC: significant changes to ensemblVEP package
VariantAnnotation ensemblVEP
23 months ago Vincent J. Carey, Jr. 6.7k
0
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5
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1.2k
views
locateVariant from VariantAnnotation returns wrong results
VariantAnnotation locateVariant
updated 2.0 years ago by 68k • written 2.0 years ago by ▴ 70
0
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0
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1.3k
views
Variant Filtering on very large VCF files
VariantAnnotation VariantFiltering
2.2 years ago Bogdan ▴ 670
2
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2
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2.1k
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
views
Docker usage with Trio Bioconductor Package
VariantAnnotation docker trio
updated 2.6 years ago by ★ 5.0k • written 2.6 years ago by • 0
4
votes
8
replies
3.0k
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 • updated 2.7 years ago davidhillis • 0
0
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0
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978
views
VariantAnnotation::readVcf incorrectly processes GATK Mutect2 vcf INFO field AS_SB_TABLE
vcf AS_SB_TABLE readVcf Mutect2 VariantAnnotation
2.8 years ago therealgenna • 0
0
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3
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2.0k
views
Add GP values to VCF
VariantAnnotation
2.9 years ago Stephanie M. Gogarten ▴ 890
0
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1
reply
2.9k
views
Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123 VariantFiltering Alignment VariantAnnotation
updated 3.1 years ago by 68k • written 3.1 years ago by ▴ 30
2
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4
replies
1.7k
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
3.3 years ago • updated 3.2 years ago rwan.work • 0
0
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2
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1.3k
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 12.9 years ago by ▴ 890
0
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3
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1.6k
views
Problem with intronic variants in VariantAnnotation
VariantAnnotation
updated 3.8 years ago by • 0 • written 4.0 years ago by • 0
0
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2
replies
1.8k
views
Reading vcf file with readVcf
VariantAnnotation
4.2 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 4.3 years ago by 16k • written 4.4 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 4.3 years ago by 6.7k • written 4.3 years ago by • 0
0
votes
1
reply
1.4k
views
GRanges object out-of-bound
VariantAnnotation
updated 4.3 years ago by 6.7k • written 4.4 years ago by • 0
2
votes
3
replies
1.6k
views
readVcf(remoteFile, "hg19", "region") works on macos, fails on linux and in docker
open.BcfFile VariantAnnotation
updated 23 months ago by • 0 • written 4.4 years ago by ▴ 470
0
votes
0
replies
916
views
Annotate mutations on DNA level to splice transcripts
VariantAnnotation
4.4 years ago Kasper_holm2 • 0
0
votes
4
replies
2.6k
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
votes
2
replies
1.8k
views
VariantAnnotation::readVcf not reading variants
VariantAnnotation
updated 4.6 years ago by 68k • written 4.6 years ago by • 0
0
votes
2
replies
3.4k
views
VCF File too large for tabix. Best option to make it usable with R?
samtools tabix VariantAnnotation VCFArray
updated 4.7 years ago by 6.7k • written 4.8 years ago by • 0
1
vote
12
replies
4.8k
views
readVcf does not recognize tabix index
VariantAnnotation readvcf tabix
updated 4.7 years ago by 6.7k • written 4.8 years ago by • 0
0
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2
replies
2.1k
views
readVCF requires the argument "genome". What does it stand for?
Genome readVcf VariantAnnotation
4.8 years ago naive • 0
2
votes
4
replies
2.1k
views
Obtaining Comments From VCF Header
VariantAnnotation VCFHeader
written 5.5 years ago by ★ 1.6k
3
votes
2
replies
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
votes
2
replies
1.8k
views
Extract structural variant and flanking sequence from VCF and fasta, in R
VariantAnnotation Bioconductor VCF Structural variants R
updated 5.7 years ago by 25k • written 5.7 years ago by • 0
0
votes
1
reply
1.0k
views
Can strand be set to minus in VRanges objects?
VariantAnnotation
updated 5.9 years ago by 68k • written 5.9 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 6.2 years ago by 25k • written 6.2 years ago by • 0
2
votes
3
replies
2.2k
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 6.4 years ago by ★ 13k • written 6.4 years ago by ▴ 30
2
votes
3
replies
1.6k
views
VariantAnnotation - subset multi-allele variants
variantAnnotation
updated 6.4 years ago by ★ 11k • written 6.4 years ago by • 0
0
votes
1
reply
1.2k
views
negative AD value interfering with readVcfasVRanges
VariantAnnotation
updated 6.5 years ago by ★ 11k • written 6.5 years ago by • 0
0
votes
3
replies
1.5k
views
rbind VCF Two Objects Column Names Error
VariantAnnotation VCF
6.5 years ago Dario Strbenac ★ 1.6k
0
votes
0
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1.2k
views
predictCoding warning message: serious or not?
software error annotation VariantAnnotation
updated 6.7 years ago by 4.2k • written 6.7 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
4.6k
views
Create protein sequences including variants from a VCF file
VariantAnnotation customProDB
updated 19 months ago by • 0 • written 6.8 years ago by ▴ 50
0
votes
1
reply
1.3k
views
VariantAnnotation fails to load VCF record
variantannotation
7.0 years ago Daniel Cameron ▴ 40
0
votes
6
replies
2.3k
views
How to prepare .vcf for seqCAT
seqCAT variantannotation gatk
updated 7.0 years ago by ▴ 30 • written 7.0 years ago by • 0
0
votes
1
reply
1.3k
views
writeVcf save invalid vcf with metadata out of order
variantannotation
updated 7.1 years ago by ★ 6.8k • written 7.1 years ago by ▴ 20
1
vote
7
replies
4.3k
views
Data from ##SAMPLE lines in VCF?
variantannotation coldata
updated 7.2 years ago by ★ 6.8k • written 7.2 years ago by ▴ 10
3
votes
3
replies
1.8k
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
votes
2
replies
1.7k
views
Error: invalid class "VRanges" object
variantannotation VRanges R Rle
updated 7.5 years ago by ★ 6.8k • written 7.5 years ago by • 0
217 results • Page 1 of 5
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Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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