Showing : variantannotation • reset
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359
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ensemblVEP deprecation and how to reproduce
VariantAnnotation
updated 5 months ago by 6.7k • written 5 months ago by • 0
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414
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Using variantAnnotation to put together genotype and consequence information
variantAnn VariantAnnotation
6 months ago ramiro.barrantes ▴ 10
1
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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 8 months ago by 52k • written 8 months ago by • 0
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0
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378
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Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
10 months ago Stevie Pederson • 0
0
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1
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461
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Is random access by row index possible for an indexed VCF file?
Rsamtools VariantAnnotation
updated 11 months ago by 68k • written 11 months ago by ▴ 180
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372
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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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878
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locateVariant from VariantAnnotation returns wrong results
VariantAnnotation locateVariant
updated 14 months ago by 68k • written 14 months ago by ▴ 70
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905
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
0
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2
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874
views
Docker usage with Trio Bioconductor Package
VariantAnnotation docker trio
updated 21 months ago by ★ 4.6k • written 21 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
23 months ago • updated 22 months ago davidhillis • 0
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741
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VariantAnnotation::readVcf incorrectly processes GATK Mutect2 vcf INFO field AS_SB_TABLE
vcf AS_SB_TABLE readVcf Mutect2 VariantAnnotation
24 months ago therealgenna • 0
0
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3
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1.6k
views
Add GP values to VCF
VariantAnnotation
2.1 years ago Stephanie M. Gogarten ▴ 890
0
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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 2.3 years ago by 68k • written 2.3 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
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
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 3.4 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 3.5 years ago by • 0
0
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1
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1.1k
views
GRanges object out-of-bound
VariantAnnotation
updated 3.5 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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778
views
Annotate mutations on DNA level to splice transcripts
VariantAnnotation
3.6 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 68k • 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 68k • 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
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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1.5k
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
832
views
Can strand be set to minus in VRanges objects?
VariantAnnotation
updated 5.1 years ago by 68k • written 5.1 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 5.6 years ago by ★ 13k • written 5.6 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
reply
978
views
negative AD value interfering with readVcfasVRanges
VariantAnnotation
updated 5.6 years ago by ★ 11k • written 5.7 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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955
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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
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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
reply
1.1k
views
VariantAnnotation fails to load VCF record
variantannotation
6.2 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
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1.1k
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
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3.7k
views
Data from ##SAMPLE lines in VCF?
variantannotation coldata
updated 6.4 years ago by ★ 6.8k • written 6.4 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
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4
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2.1k
views
Problem when transforming Platypus vcf to VRanges
variantannotation vcf readvcf vranges
updated 6.6 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
replies
1.5k
views
VariantAnnotation::locateVariants error coming from XVector
variantannotation xvector iranges
6.7 years ago Vivek.b ▴ 100
0
votes
2
replies
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
50 results • Page 1 of 1
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Answer: DESeq2 adujsted p-value cutoff seemingly not working by James W. MacDonald 68k
From `?results' ``` On p-values: By default, independent filtering is performed to select a set of genes for multiple tes…
Comment: Issue with assigning transcript IDs to reads when using summarizeOverlaps(mode = by SofieK • 0
Thank you, I will try this and see.
Comment: DiffBind - question on the use of filtered or unfiltered input data by deltaexploitss • 0
Data input is the adding of data into a computer. This can take place through an input device such as a keyboard. A user inputs data, which…
Comment: GenomeInfoDbData cannot install in R and warning had non-zero exit status by Renuka • 0
how you did it pls explain
Answer: Issue with assigning transcript IDs to reads when using summarizeOverlaps(mode = by James W. MacDonald 68k
If I understand correctly, you want to assess differential transcript abundances. If so, there are a couple of ways you can do that. One wa…
Votes
A: Effect of lfcThreshold on p-value in DESeq2
Answer: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
Answer: Issue with assigning transcript IDs to reads when using summarizeOverlaps(mode =
Comment: Unused arguments error without used arguments in GSVA?
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