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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372
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Using variantAnnotation to put together genotype and consequence information
variantAnn VariantAnnotation
4 months ago ramiro.barrantes ▴ 10
1
vote
2
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986
views
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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0
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335
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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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423
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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346
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RFC: significant changes to ensemblVEP package
VariantAnnotation ensemblVEP
11 months ago Vincent J. Carey, Jr. 6.7k
0
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5
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827
views
locateVariant from VariantAnnotation returns wrong results
VariantAnnotation locateVariant
updated 12 months ago by 67k • written 12 months ago by ▴ 70
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845
views
Variant Filtering on very large VCF files
VariantAnnotation VariantFiltering
14 months ago Bogdan ▴ 670
2
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2
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1.8k
views
Matching Variants Between Two VCF Objects
VariantAnnotation
written 4.0 years ago by ★ 1.5k
0
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2
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831
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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706
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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
views
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
replies
1.2k
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
2.2 years ago rwan.work • 0
0
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2
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1.0k
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
2.2 years ago rwan.work • 0
0
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2
replies
2.9k
views
merging VCF files
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
written 11.9 years ago by ▴ 870
0
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3
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1.2k
views
Problem with intronic variants in VariantAnnotation
VariantAnnotation
updated 2.8 years ago by • 0 • written 2.9 years ago by • 0
0
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2
replies
1.4k
views
Reading vcf file with readVcf
VariantAnnotation
3.2 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 3.3 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
views
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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744
views
Annotate mutations on DNA level to splice transcripts
VariantAnnotation
3.4 years ago Kasper_holm2 • 0
0
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4
replies
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
replies
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
replies
3.8k
views
readVcf does not recognize tabix index
VariantAnnotation readvcf tabix
updated 3.7 years ago by 6.7k • written 3.7 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
3.7 years ago naive • 0
2
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4
replies
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 4.6 years ago by 25k • written 4.6 years ago by ★ 1.5k
0
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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
803
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
reply
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
replies
1.2k
views
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
reply
943
views
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
replies
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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927
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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
replies
1.7k
views
Error in VCF parsing with VariantAnnotation
software error VariantAnnotation ensemblVEP
updated 5.7 years ago by ★ 6.8k • written 5.8 years ago by ▴ 20
4
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9
replies
3.7k
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
replies
1.8k
views
How to prepare .vcf for seqCAT
seqCAT variantannotation gatk
updated 6.0 years ago by ▴ 30 • written 6.0 years ago by • 0
0
votes
1
reply
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
replies
1.5k
views
Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
variantannotation
updated 6.4 years ago by ★ 6.8k • written 6.5 years ago by ▴ 10
3
votes
4
replies
2.0k
views
Problem when transforming Platypus vcf to VRanges
variantannotation vcf readvcf vranges
updated 6.4 years ago by ★ 11k • written 6.4 years ago by • 0
0
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2
replies
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
replies
1.4k
views
VariantAnnotation::locateVariants error coming from XVector
variantannotation xvector iranges
6.5 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: p value is 0, padj is 0 by Michael Love 43k
``` > set.seed(1); t.test(rnorm(200,rep(c(0,80),each=100)) ~ rep(0:1,each=100))$p.value [1] 0 ```
Answer: Cannot install GO.db and org.Hs.eg.db by James W. MacDonald 67k
You might try tracing the namespace loading. ``` Sys.setenv("_R_TRACE_LOADNAMESPACE_"="2") install("org.Hs.eg.db") ``` And see if th…
Answer: p value is 0, padj is 0 by James W. MacDonald 67k
It is quite possible for a very small p-value to remain very small after multiplicity adjustment. I don't know the cutoff for `DESeq2` to r…
Answer: Help using rtracklayer for gene ID extraction by James W. MacDonald 67k
You don't need `rtracklayer` for this (not directly anyway), but instead you need `txdbmaker` which you can use to make a `TxDb` object tha…
Answer: Feature Counts - potential bug with outfile.jcounts by Wei Shi ★ 3.6k
We will further develop the junction quantification module to support the use of user-provided annotation data for annotating detected junc…
Votes
Answer: Feature Counts - potential bug with outfile.jcounts
Answer: Feature Counts - potential bug with outfile.jcounts
Answer: Pre-filtering TPM kallisto for ssGSEA / DESeq2
Answer: Mapping Between GenBank ID's and Uniprot
Comment: What type of counts data to import for performing Isoform analysis in edgeR
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