Showing : variantAnnotation • reset
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307
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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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377
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Using variantAnnotation to put together genotype and consequence information
variantAnn VariantAnnotation
5 months ago ramiro.barrantes ▴ 10
1
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2
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1.0k
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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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341
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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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429
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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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350
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RFC: significant changes to ensemblVEP package
VariantAnnotation ensemblVEP
11 months ago Vincent J. Carey, Jr. 6.7k
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5
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842
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locateVariant from VariantAnnotation returns wrong results
VariantAnnotation locateVariant
updated 12 months ago by 67k • written 12 months ago by ▴ 70
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852
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Variant Filtering on very large VCF files
VariantAnnotation VariantFiltering
15 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 4.1 years ago by ★ 1.5k
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2
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835
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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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710
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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
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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
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1.3k
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
2.3 years ago rwan.work • 0
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2
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1.0k
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
2.3 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 12.0 years ago by ▴ 870
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3
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1.3k
views
Problem with intronic variants in VariantAnnotation
VariantAnnotation
updated 2.8 years ago by • 0 • written 3.0 years ago by • 0
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2
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1.4k
views
Reading vcf file with readVcf
VariantAnnotation
3.3 years ago • updated 3.2 years ago aurelien.dejode • 0
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2
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1.0k
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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
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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 3.5 years ago by ▴ 470
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0
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750
views
Annotate mutations on DNA level to splice transcripts
VariantAnnotation
3.4 years ago Kasper_holm2 • 0
0
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4
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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
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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
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3.8k
views
readVcf does not recognize tabix index
VariantAnnotation readvcf tabix
updated 3.7 years ago by 6.7k • written 3.8 years ago by • 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
3.8 years ago naive • 0
2
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4
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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 4.7 years ago by 25k • written 4.7 years ago by ★ 1.5k
0
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2
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1.4k
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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
813
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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1.8k
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 5.4 years ago by ★ 13k • written 5.4 years ago by ▴ 30
2
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3
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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
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947
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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
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1.2k
views
rbind VCF Two Objects Column Names Error
VariantAnnotation VCF
5.6 years ago Dario Strbenac ★ 1.5k
0
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0
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931
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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
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1.7k
views
Error in VCF parsing with VariantAnnotation
software error VariantAnnotation ensemblVEP
updated 5.8 years ago by ★ 6.8k • written 5.8 years ago by ▴ 20
4
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9
replies
3.8k
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
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1.8k
views
How to prepare .vcf for seqCAT
seqCAT variantannotation gatk
updated 6.1 years ago by ▴ 30 • written 6.1 years ago by • 0
0
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1
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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
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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
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3
replies
1.5k
views
Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
variantannotation
updated 6.5 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 6.5 years ago by ★ 11k • written 6.5 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 6.5 years ago by ★ 6.8k • written 6.5 years ago by • 0
0
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2
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1.4k
views
VariantAnnotation::locateVariants error coming from XVector
variantannotation xvector iranges
6.6 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
Recent ...
Replies
Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
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C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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