Showing : VariantAnnotation • reset
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158
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Problem using locateVariants() from the VariantAnnotation package
VariantAnnotation vari
11 days ago • updated 9 days ago Marco • 0
0
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1
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404
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ensemblVEP deprecation and how to reproduce
VariantAnnotation
updated 6 months ago by 6.7k • written 6 months ago by • 0
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0
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457
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Using variantAnnotation to put together genotype and consequence information
variantAnn VariantAnnotation
7 months ago ramiro.barrantes ▴ 10
1
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2
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1.4k
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How to compare subset of samples from VCF files
VCF VariantAnnotation
updated 9 months ago by 52k • written 9 months ago by • 0
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0
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430
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Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
11 months ago Stevie Pederson • 0
0
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1
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487
views
Is random access by row index possible for an indexed VCF file?
Rsamtools VariantAnnotation
updated 12 months ago by 68k • written 12 months ago by ▴ 180
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0
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389
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RFC: significant changes to ensemblVEP package
VariantAnnotation ensemblVEP
14 months ago Vincent J. Carey, Jr. 6.7k
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5
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909
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locateVariant from VariantAnnotation returns wrong results
VariantAnnotation locateVariant
updated 15 months ago by 68k • written 15 months ago by ▴ 70
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956
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Variant Filtering on very large VCF files
VariantAnnotation VariantFiltering
17 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 4.3 years ago by ★ 1.6k
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2
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905
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Docker usage with Trio Bioconductor Package
VariantAnnotation docker trio
updated 22 months ago by ★ 4.7k • written 22 months ago by • 0
4
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8
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2.3k
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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
24 months ago davidhillis • 0
0
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0
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771
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VariantAnnotation::readVcf incorrectly processes GATK Mutect2 vcf INFO field AS_SB_TABLE
vcf AS_SB_TABLE readVcf Mutect2 VariantAnnotation
2.1 years ago therealgenna • 0
0
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3
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1.7k
views
Add GP values to VCF
VariantAnnotation
2.2 years ago Stephanie M. Gogarten ▴ 890
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1
reply
2.2k
views
Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123 VariantFiltering Alignment VariantAnnotation
updated 2.3 years ago by 68k • written 2.3 years ago by ▴ 30
2
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4
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1.4k
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
2.5 years ago rwan.work • 0
0
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2
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1.1k
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
2.5 years ago rwan.work • 0
0
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2
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3.0k
views
merging VCF files
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
written 12.2 years ago by ▴ 890
0
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3
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1.3k
views
Problem with intronic variants in VariantAnnotation
VariantAnnotation
updated 3.0 years ago by • 0 • written 3.2 years ago by • 0
0
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2
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1.5k
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Reading vcf file with readVcf
VariantAnnotation
3.5 years ago aurelien.dejode • 0
0
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2
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1.1k
views
Multiple exons for predictCoding() from VariantAnnotation (use phase information from gff3 file)?
VariantAnnotation
updated 3.5 years ago by 16k • written 3.6 years ago by • 0
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 3.5 years ago by 6.7k • written 3.6 years ago by • 0
0
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1
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1.2k
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GRanges object out-of-bound
VariantAnnotation
updated 3.5 years ago by 6.7k • written 3.6 years ago by • 0
2
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3
replies
1.4k
views
readVcf(remoteFile, "hg19", "region") works on macos, fails on linux and in docker
open.BcfFile VariantAnnotation
updated 13 months ago by • 0 • written 3.7 years ago by ▴ 470
0
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0
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796
views
Annotate mutations on DNA level to splice transcripts
VariantAnnotation
3.7 years ago Kasper_holm2 • 0
0
votes
4
replies
2.2k
views
Error of read in large vcf file using readVcf
SomaticSignatures VariantAnnotation
updated 3.7 years ago by 68k • written 3.7 years ago by • 0
0
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2
replies
1.5k
views
VariantAnnotation::readVcf not reading variants
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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2.9k
views
VCF File too large for tabix. Best option to make it usable with R?
samtools tabix VariantAnnotation VCFArray
updated 3.9 years ago by 6.7k • written 4.0 years ago by • 0
1
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12
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4.1k
views
readVcf does not recognize tabix index
VariantAnnotation readvcf tabix
updated 3.9 years ago by 6.7k • written 4.0 years ago by • 0
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
4.0 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 4.7 years ago by ★ 1.6k
3
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2
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1.7k
views
Import or Subset VCF PASS Variants
VariantAnnotation subset ScanVcfParam
updated 4.9 years ago by 25k • written 4.9 years ago by ★ 1.6k
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2
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1.5k
views
Extract structural variant and flanking sequence from VCF and fasta, in R
VariantAnnotation Bioconductor VCF Structural variants R
updated 4.9 years ago by 25k • written 4.9 years ago by • 0
0
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1
reply
859
views
Can strand be set to minus in VRanges objects?
VariantAnnotation
updated 5.2 years ago by 68k • written 5.2 years ago by • 0
0
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1
reply
1.6k
views
FilterVCF Filter '' failed: shape of 'skeleton' is not compatible with 'NROW(flesh)'
variantAnnotation
updated 5.4 years ago by 25k • written 5.4 years ago by • 0
2
votes
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 5.6 years ago by ★ 13k • written 5.6 years ago by ▴ 30
2
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3
replies
1.3k
views
VariantAnnotation - subset multi-allele variants
variantAnnotation
updated 5.7 years ago by ★ 11k • written 5.7 years ago by • 0
0
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1
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1.0k
views
negative AD value interfering with readVcfasVRanges
VariantAnnotation
updated 5.7 years ago by ★ 11k • written 5.8 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
5.8 years ago Dario Strbenac ★ 1.6k
0
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0
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986
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predictCoding warning message: serious or not?
software error annotation VariantAnnotation
updated 5.9 years ago by 4.1k • written 5.9 years ago by • 0
2
votes
3
replies
1.9k
views
Error in VCF parsing with VariantAnnotation
software error VariantAnnotation ensemblVEP
updated 6.0 years ago by ★ 6.8k • written 6.0 years ago by ▴ 20
4
votes
9
replies
4.0k
views
Create protein sequences including variants from a VCF file
VariantAnnotation customProDB
updated 9 months ago by • 0 • written 6.0 years ago by ▴ 50
0
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1
reply
1.1k
views
VariantAnnotation fails to load VCF record
variantannotation
6.2 years ago Daniel Cameron ▴ 40
0
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6
replies
2.0k
views
How to prepare .vcf for seqCAT
seqCAT variantannotation gatk
updated 6.3 years ago by ▴ 30 • written 6.3 years ago by • 0
0
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1
reply
1.1k
views
writeVcf save invalid vcf with metadata out of order
variantannotation
updated 6.3 years ago by ★ 6.8k • written 6.3 years ago by ▴ 20
1
vote
7
replies
3.8k
views
Data from ##SAMPLE lines in VCF?
variantannotation coldata
updated 6.4 years ago by ★ 6.8k • written 6.5 years ago by ▴ 10
3
votes
3
replies
1.6k
views
Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
variantannotation
updated 6.7 years ago by ★ 6.8k • written 6.7 years ago by ▴ 10
3
votes
4
replies
2.1k
views
Problem when transforming Platypus vcf to VRanges
variantannotation vcf readvcf vranges
updated 6.7 years ago by ★ 11k • written 6.7 years ago by • 0
0
votes
2
replies
1.4k
views
Error: invalid class "VRanges" object
variantannotation VRanges R Rle
updated 6.7 years ago by ★ 6.8k • written 6.7 years ago by • 0
0
votes
2
replies
1.5k
views
VariantAnnotation::locateVariants error coming from XVector
variantannotation xvector iranges
6.8 years ago Vivek.b ▴ 100
50 results • Page 1 of 1
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If you just have the transcript data, you probably don't need (and maybe cannot use) `tximport`. Instead you could just do the naive thing …
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Setting aside the inadvisability of putting these data into Excel (and I should point out that these data are not single-cell, but instead …
Comment: concentration tables suitable as input for new packages? by wilkinson • 0
I am grateful for your response. Software such as "Spectra" may parse MS-data to generate tables of concentrations, for instance. But inste…
Comment: Removing UTR from GTF for gene quantification by ATpoint ★ 4.7k
Consider asking at biostars or bioinformatics reddit, since this is not directly related to a Bioconductor problem. Anyway, a couple of th…
Comment: Combining RNAseq and microarray data using edgeR/limma-voom by Hoover • 0
I got it! ([Drift Boss][1]) [1]: https://driftbossgame.co
Votes
Answer: Differential expression of proteins using somascan data
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