Showing : VariantAnnotation • reset
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21
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GRanges object out-of-bound
VariantAnnotation
4 days ago Kasper_holm2 • 0
0
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1
reply
76
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Multiple exons for predictCoding() from VariantAnnotation (use phase information from gff3 file)?
VariantAnnotation
7 days ago • updated 5 days ago Kasper_holm2 • 0
2
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3
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177
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readVcf(remoteFile, "hg19", "region") works on macos, fails on linux and in docker
open.BcfFile VariantAnnotation
updated 10 days ago by • 0 • written 17 days ago by ▴ 460
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0
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51
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Annotate mutations on DNA level to splice transcripts
VariantAnnotation
12 days ago • updated 11 days ago Kasper_holm2 • 0
0
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4
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112
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Error of read in large vcf file using readVcf
SomaticSignatures VariantAnnotation
updated 26 days ago by 57k • written 27 days ago by • 0
0
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2
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148
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VariantAnnotation::readVcf not reading variants
VariantAnnotation
updated 9 weeks ago by 57k • written 9 weeks ago by • 0
0
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2
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253
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VCF File too large for tabix. Best option to make it usable with R?
samtools tabix VariantAnnotation VCFArray
updated 3 months ago by 6.5k • written 4 months ago by • 0
1
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12
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377
views
readVcf does not recognize tabix index
VariantAnnotation readvcf tabix
updated 3 months ago by 6.5k • written 4 months ago by • 0
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2
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127
views
readVCF requires the argument "genome". What does it stand for?
Genome readVcf VariantAnnotation
4 months ago naive • 0
1
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1
reply
155
views
Matching Variants Between Two VCF Objects
VariantAnnotation
updated 7 months ago by ▴ 90 • written 8 months ago by ★ 1.5k
2
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2
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183
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Obtaining Comments From VCF Header
VariantAnnotation VCFHeader
updated 13 months ago by 25k • written 13 months ago by ★ 1.5k
3
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2
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189
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Import or Subset VCF PASS Variants
VariantAnnotation subset ScanVcfParam
updated 15 months ago by 25k • written 15 months ago by ★ 1.5k
0
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2
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157
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Extract structural variant and flanking sequence from VCF and fasta, in R
VariantAnnotation Bioconductor VCF Structural variants R
updated 15 months ago by 25k • written 15 months ago by • 0
0
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1
reply
106
views
Can strand be set to minus in VRanges objects?
VariantAnnotation
updated 18 months ago by 57k • written 18 months ago by • 0
0
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1
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253
views
FilterVCF Filter '' failed: shape of 'skeleton' is not compatible with 'NROW(flesh)'
variantAnnotation
updated 21 months ago by 25k • written 21 months ago by • 0
2
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3
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419
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"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 2.0 years ago by 13k • written 2.0 years ago by ▴ 30
2
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3
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216
views
VariantAnnotation - subset multi-allele variants
variantAnnotation
updated 2.0 years ago by 11k • written 2.0 years ago by • 0
0
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1
reply
215
views
negative AD value interfering with readVcfasVRanges
VariantAnnotation
updated 2.1 years ago by 11k • written 2.1 years ago by • 0
0
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3
replies
318
views
rbind VCF Two Objects Column Names Error
VariantAnnotation VCF
2.1 years ago Dario Strbenac ★ 1.5k
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0
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261
views
predictCoding warning message: serious or not?
software error annotation VariantAnnotation
updated 2.3 years ago by 2.8k • written 2.3 years ago by • 0
2
votes
3
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397
views
Error in VCF parsing with VariantAnnotation
software error VariantAnnotation ensemblVEP
updated 2.4 years ago by ★ 6.7k • written 2.4 years ago by ▴ 20
3
votes
8
replies
501
views
Create protein sequences including variants from a VCF file
VariantAnnotation customProDB
2.4 years ago daniel.magnus.bader ▴ 40
0
votes
1
reply
366
views
VariantAnnotation fails to load VCF record
variantannotation
2.6 years ago Daniel Cameron ▴ 20
0
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6
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479
views
How to prepare .vcf for seqCAT
seqCAT variantannotation gatk
updated 2.7 years ago by ▴ 30 • written 2.7 years ago by • 0
0
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1
reply
313
views
writeVcf save invalid vcf with metadata out of order
variantannotation
updated 2.7 years ago by ★ 6.7k • written 2.7 years ago by ▴ 20
1
vote
7
replies
1.0k
views
Data from ##SAMPLE lines in VCF?
variantannotation coldata
updated 2.8 years ago by ★ 6.7k • written 2.8 years ago by ▴ 10
3
votes
3
replies
523
views
Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
variantannotation
updated 3.1 years ago by ★ 6.7k • written 3.1 years ago by ▴ 10
3
votes
4
replies
551
views
Problem when transforming Platypus vcf to VRanges
variantannotation vcf readvcf vranges
updated 3.1 years ago by 11k • written 3.1 years ago by • 0
0
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2
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476
views
Error: invalid class "VRanges" object
variantannotation VRanges R Rle
updated 3.1 years ago by ★ 6.7k • written 3.1 years ago by • 0
0
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2
replies
532
views
VariantAnnotation::locateVariants error coming from XVector
variantannotation xvector iranges
3.2 years ago Vivek.b ▴ 100
0
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2
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458
views
filtering a VCF file based on genotype
variantannotation
updated 3.2 years ago by ★ 6.7k • written 3.2 years ago by ▴ 620
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1
reply
443
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VariantAnnotation and filtering a VCF
variantannotation
3.2 years ago Bogdan ▴ 620
0
votes
1
reply
457
views
Annotating outdated SNP identifiers
variants variantannotation SNPlocs.Hsapiens.dbSNP150.GRCh38 biomaRt
3.4 years ago sandmann.t ▴ 70
2
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2
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572
views
[VariantAnnotation] Preserve query metadata with locateVariants()
variantannotation locatevariants metadata mcols
updated 3.6 years ago by ★ 6.7k • written 3.6 years ago by ▴ 570
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2
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2.1k
views
Problem using biocLite() to update packages
biocLite BiocInstaller variantannotation
updated 3.7 years ago by 57k • written 3.7 years ago by ★ 2.0k
0
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1
reply
604
views
predictCoding errors with: sequence ^1$ not found
variantannotation predict coding locateVariants granges
3.8 years ago tony j • 0
7
votes
4
replies
1.1k
views
BiocGenerics built with R 3.4.2 changes behaviour
biocgenerics iranges variantannotation
updated 3.8 years ago by 15k • written 3.8 years ago by ▴ 40
7
votes
6
replies
893
views
SNP location annotation problem in "VariantAnnotation" package
annotation variantannotation
updated 3.9 years ago by ★ 6.7k • written 3.9 years ago by ▴ 20
0
votes
4
replies
790
views
Translation Error in predictCoding() for VariantAnnotation
VariantAnnotation
updated 3.9 years ago by 15k • written 3.9 years ago by • 0
8
votes
6
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1.0k
views
Error when running "locateVariants" function in "VariantAnnotation" package
variantannotation tidyverse genomicfeatures
updated 3.9 years ago by 15k • written 3.9 years ago by ▴ 20
0
votes
2
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820
views
locateVariants function does not find an annotation for the locus
locatevariants txdb.hsapiens.ucsc.hg19.knowngene variantannotation
3.9 years ago Aleksandra • 0
0
votes
1
reply
852
views
Troubleshooting a histogram DataTrack in Gviz
VariantAnnotation gviz
4.0 years ago Russ Fraser ▴ 20
2
votes
5
replies
1.5k
views
VariantAnnotation: Error with ScanVcfParam
variantannotation vcf readvcf filtervcf scanvcfparam
4.0 years ago Didi ▴ 10
0
votes
2
replies
630
views
SNPs in multiple locations
txdb.hsapiens.ucsc.hg19.knowngene ucsc annotation locatevariants variantannotation
updated 4.1 years ago by ★ 6.7k • written 4.1 years ago by • 0
0
votes
1
reply
478
views
summarizeVariants from VariantAnnotation reordering genes in rownames
variantannotation summarizevariants
updated 4.1 years ago by ★ 6.7k • written 4.1 years ago by • 0
3
votes
4
replies
688
views
No annotation for single SNPs
variantannotation SNPs txdb.hsapiens.ucsc.hg19.knowngene ucsc
updated 4.1 years ago by ★ 6.7k • written 4.1 years ago by • 0
0
votes
6
replies
1.2k
views
Error using readVcf
gwastools variantannotation
updated 4.1 years ago by ▴ 800 • written 4.1 years ago by • 0
3
votes
3
replies
1.3k
views
VariantAnnotation Installation Failure
VariantAnnotation
updated 4.2 years ago by ★ 6.7k • written 4.2 years ago by ▴ 340
1
vote
2
replies
498
views
Exclude Mutations from Mutation List
variantannotation
updated 4.2 years ago by 25k • written 4.2 years ago by ▴ 110
2
votes
6
replies
1.2k
views
extracting Allele Read Counts - part2
rsamtools variantannotation
updated 4.3 years ago by 57k • written 4.3 years ago by ▴ 620
50 results • Page 1 of 1
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Comment: Best practice for quantifying sncRNA by Abhishek • 0
I wonder what would be a good metric to assess the quantification quality
Comment: Best practice for quantifying sncRNA by Abhishek • 0
Thank you for sharing your thoughts. I used Salmon and indexed using hg38 gencodes transcriptome. After the tximport step, I ended up gett…
Comment: DESeq2 question: why I got discrepancy results for DEGs when using different way by Ming ▴ 350
Thx so much for the diagnosis and advice. Indeed, in my data, some genes have all 0 for all sampes of a contrast for both "Mut" and "WT" gr…
Comment: Best practice for quantifying sncRNA by Steve Lianoglou 13k
> It's my opinion that miRNA is a mirage intended to make MDs salivate and biostatisticians wail in misery, but what do I know? I'll tell …
Comment: Idea: Using DESeq2 to test a change in ratio of two genes by Michael Love 33k
Yes, it's true that we take the reference gene(s) as a noise free measurement of the reference variation with this approach, and control ag…
Votes
Comment: Idea: Using DESeq2 to test a change in ratio of two genes
Time Series Analysis
Comment: Time series DE gene analysis with edgeR where specific timepoints have NA levels
Comment: Time series DE gene analysis with edgeR where specific timepoints have NA levels
Answer: Time series DE gene analysis with edgeR where specific timepoints have NA levels
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