Showing : VariantAnnotation • reset
0
votes
3
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153
views
Add GP values to VCF
VariantAnnotation
27 days ago • updated 22 days ago Stephanie M. Gogarten ▴ 820
0
votes
1
reply
290
views
Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123 VariantFiltering Alignment VariantAnnotation
updated 12 weeks ago by 62k • written 3 months ago by • 0
2
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4
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321
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
4 months ago rwan.work • 0
0
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2
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180
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
4 months ago rwan.work • 0
0
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2
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1.9k
views
merging VCF files
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
written 10.1 years ago by ▴ 820
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3
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534
views
Problem with intronic variants in VariantAnnotation
VariantAnnotation
updated 11 months ago by • 0 • written 13 months ago by • 0
0
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2
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421
views
Reading vcf file with readVcf
VariantAnnotation
16 months ago aurelien.dejode • 0
0
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2
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404
views
Multiple exons for predictCoding() from VariantAnnotation (use phase information from gff3 file)?
VariantAnnotation
updated 17 months ago by 16k • written 18 months ago by • 0
0
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5
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701
views
installation error: Error in setIs(class2, cli, extensionObject = obji, doComplete = FALSE and setClass() for chromVAR and VariantAnnotation
Install VariantAnnotation Bioconductor chromVAR
updated 17 months ago by 6.6k • written 17 months ago by • 0
0
votes
1
reply
396
views
GRanges object out-of-bound
VariantAnnotation
updated 17 months ago by 6.6k • written 18 months ago by • 0
2
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3
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582
views
readVcf(remoteFile, "hg19", "region") works on macos, fails on linux and in docker
open.BcfFile VariantAnnotation
updated 14 months ago by • 0 • written 19 months ago by ▴ 470
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0
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300
views
Annotate mutations on DNA level to splice transcripts
VariantAnnotation
18 months ago Kasper_holm2 • 0
0
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4
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592
views
Error of read in large vcf file using readVcf
SomaticSignatures VariantAnnotation
updated 19 months ago by 62k • written 19 months ago by • 0
0
votes
2
replies
610
views
VariantAnnotation::readVcf not reading variants
VariantAnnotation
updated 20 months ago by 62k • written 20 months ago by • 0
0
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2
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1.2k
views
VCF File too large for tabix. Best option to make it usable with R?
samtools tabix VariantAnnotation VCFArray
updated 22 months ago by 6.6k • written 23 months ago by • 0
1
vote
12
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1.5k
views
readVcf does not recognize tabix index
VariantAnnotation readvcf tabix
updated 22 months ago by 6.6k • written 22 months ago by • 0
0
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2
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516
views
readVCF requires the argument "genome". What does it stand for?
Genome readVcf VariantAnnotation
22 months ago naive • 0
2
votes
1
reply
678
views
Matching Variants Between Two VCF Objects
VariantAnnotation
updated 2.2 years ago by ▴ 100 • written 2.2 years ago by ★ 1.5k
2
votes
2
replies
549
views
Obtaining Comments From VCF Header
VariantAnnotation VCFHeader
updated 2.6 years ago by 25k • written 2.6 years ago by ★ 1.5k
3
votes
2
replies
650
views
Import or Subset VCF PASS Variants
VariantAnnotation subset ScanVcfParam
updated 2.8 years ago by 25k • written 2.8 years ago by ★ 1.5k
0
votes
2
replies
576
views
Extract structural variant and flanking sequence from VCF and fasta, in R
VariantAnnotation Bioconductor VCF Structural variants R
updated 2.8 years ago by 25k • written 2.8 years ago by • 0
0
votes
1
reply
327
views
Can strand be set to minus in VRanges objects?
VariantAnnotation
updated 3.1 years ago by 62k • written 3.1 years ago by • 0
0
votes
1
reply
604
views
FilterVCF Filter '' failed: shape of 'skeleton' is not compatible with 'NROW(flesh)'
variantAnnotation
updated 3.3 years ago by 25k • written 3.3 years ago by • 0
2
votes
3
replies
903
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 3.5 years ago by 13k • written 3.5 years ago by ▴ 30
2
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3
replies
451
views
VariantAnnotation - subset multi-allele variants
variantAnnotation
updated 3.6 years ago by 11k • written 3.6 years ago by • 0
0
votes
1
reply
431
views
negative AD value interfering with readVcfasVRanges
VariantAnnotation
updated 3.6 years ago by 11k • written 3.7 years ago by • 0
0
votes
3
replies
605
views
rbind VCF Two Objects Column Names Error
VariantAnnotation VCF
3.7 years ago Dario Strbenac ★ 1.5k
0
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0
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466
views
predictCoding warning message: serious or not?
software error annotation VariantAnnotation
updated 3.8 years ago by 3.4k • written 3.8 years ago by • 0
2
votes
3
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881
views
Error in VCF parsing with VariantAnnotation
software error VariantAnnotation ensemblVEP
updated 3.9 years ago by ★ 6.7k • written 3.9 years ago by ▴ 20
3
votes
8
replies
1.7k
views
Create protein sequences including variants from a VCF file
VariantAnnotation customProDB
3.9 years ago daniel.magnus.bader ▴ 40
0
votes
1
reply
607
views
VariantAnnotation fails to load VCF record
variantannotation
4.2 years ago Daniel Cameron ▴ 40
0
votes
6
replies
969
views
How to prepare .vcf for seqCAT
seqCAT variantannotation gatk
updated 4.2 years ago by ▴ 30 • written 4.2 years ago by • 0
0
votes
1
reply
514
views
writeVcf save invalid vcf with metadata out of order
variantannotation
updated 4.2 years ago by ★ 6.7k • written 4.2 years ago by ▴ 20
1
vote
7
replies
2.1k
views
Data from ##SAMPLE lines in VCF?
variantannotation coldata
updated 4.3 years ago by ★ 6.7k • written 4.4 years ago by ▴ 10
3
votes
3
replies
774
views
Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
variantannotation
updated 4.6 years ago by ★ 6.7k • written 4.6 years ago by ▴ 10
3
votes
4
replies
1.1k
views
Problem when transforming Platypus vcf to VRanges
variantannotation vcf readvcf vranges
updated 4.6 years ago by 11k • written 4.6 years ago by • 0
0
votes
2
replies
728
views
Error: invalid class "VRanges" object
variantannotation VRanges R Rle
updated 4.6 years ago by ★ 6.7k • written 4.6 years ago by • 0
0
votes
2
replies
817
views
VariantAnnotation::locateVariants error coming from XVector
variantannotation xvector iranges
4.7 years ago Vivek.b ▴ 100
0
votes
2
replies
900
views
filtering a VCF file based on genotype
variantannotation
updated 4.7 years ago by ★ 6.7k • written 4.7 years ago by ▴ 660
0
votes
1
reply
685
views
VariantAnnotation and filtering a VCF
variantannotation
4.7 years ago Bogdan ▴ 660
0
votes
1
reply
689
views
Annotating outdated SNP identifiers
variants variantannotation SNPlocs.Hsapiens.dbSNP150.GRCh38 biomaRt
4.9 years ago sandmann.t ▴ 70
2
votes
2
replies
857
views
[VariantAnnotation] Preserve query metadata with locateVariants()
variantannotation locatevariants metadata mcols
updated 5.1 years ago by ★ 6.7k • written 5.1 years ago by ▴ 650
0
votes
2
replies
2.4k
views
Problem using biocLite() to update packages
biocLite BiocInstaller variantannotation
updated 5.2 years ago by 62k • written 5.2 years ago by ★ 2.0k
0
votes
1
reply
831
views
predictCoding errors with: sequence ^1$ not found
variantannotation predict coding locateVariants granges
5.3 years ago tony j • 0
7
votes
4
replies
1.5k
views
BiocGenerics built with R 3.4.2 changes behaviour
biocgenerics iranges variantannotation
updated 5.3 years ago by 16k • written 5.4 years ago by ▴ 40
7
votes
6
replies
1.3k
views
SNP location annotation problem in "VariantAnnotation" package
annotation variantannotation
updated 5.4 years ago by ★ 6.7k • written 5.4 years ago by ▴ 20
0
votes
4
replies
1.2k
views
Translation Error in predictCoding() for VariantAnnotation
VariantAnnotation
updated 5.4 years ago by 16k • written 5.4 years ago by • 0
8
votes
6
replies
1.5k
views
Error when running "locateVariants" function in "VariantAnnotation" package
variantannotation tidyverse genomicfeatures
updated 5.4 years ago by 16k • written 5.4 years ago by ▴ 20
0
votes
2
replies
1.1k
views
locateVariants function does not find an annotation for the locus
locatevariants txdb.hsapiens.ucsc.hg19.knowngene variantannotation
5.5 years ago Aleksandra • 0
0
votes
1
reply
1.1k
views
Troubleshooting a histogram DataTrack in Gviz
VariantAnnotation gviz
5.5 years ago Russ Fraser ▴ 30
50 results • Page 1 of 1
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Answer: struggling to create a heatmap by ATpoint ★ 2.1k
I am reluctant to read through that wall of code. Here is what would work. Note that prefiltering makes sense before, not after running `DE…
Answer: collapseReplicates error after tximeta by Michael Love 39k
The issue is that `collapseReplicates` just collapses `counts` and doesn't account for multiple assays which you need for e.g. Swish or oth…
Comment: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it by ATpoint ★ 2.1k
That having said, I recommend to inspect the MA-plots (`plotMA()`), at best the ones produced right from `res <- results(dds); plotMA(res)`…
Answer: Which genes are outliers in DESeq2? by ATpoint ★ 2.1k
You can take over some of the lines from `results()` to find them easily: ```r suppressPackageStartupMessages(library(DESeq2)) set.s…
Answer: Which genes are outliers in DESeq2? by Michael Love 39k
Outliers will have high maxCooks values in `mcols(dds)` -- the threshold is `qf(.99, p, n - p)` where n is sample size and p is number of c…
Votes
Significant reporter activity with mpralm function
Answer: I cannot install annotables package in Rstudio (macOS)
Answer: log2 of normalized counts for further analyzes
Answer: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
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