Showing : variantannotation • reset
0
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11
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1.4k
views
Complete variant toolbox: gmapR/VariantTools/VariantAnnotation
VariantAnnotation Annotation VariantAnnotation VariantTools VariantAnnotation Annotation
updated 9.2 years ago by ★ 6.7k • written 9.2 years ago by ★ 1.7k
4
votes
11
replies
1.2k
views
Filter every X position
variantannotation
8.1 years ago remi.tournebize ▴ 10
5
votes
6
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2.6k
views
Error in reading 1000 genomes data
variantannotation
updated 6.9 years ago by 25k • written 8.2 years ago by ▴ 20
2
votes
6
replies
2.8k
views
Import of vcf with VariantAnnotation
variantannotation somaticsignatures
8.3 years ago Anna N. • 0
1
vote
5
replies
3.5k
views
Converting a DNAStringSetList to characters quickly
readVcf DNAStringSet DNAStringSetList variantannotation readvcf
7.8 years ago dan.gatti • 0
0
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7
replies
1.3k
views
mutant allele read counts
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
updated 8.7 years ago by ★ 6.7k • written 8.7 years ago by ★ 12k
0
votes
5
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1.2k
views
Complete variant toolbox: gmapR/VariantTools/VariantAnnotation
BiocViews VariantAnnotation Annotation biocViews Rsubread VariantAnnotation gmapR BiocViews
9.2 years ago • updated 9.1 years ago Thomas Girke ★ 1.7k
0
votes
17
replies
1.8k
views
problems with strand in predictCoding
VariantAnnotation Annotation BSgenome BSgenome VariantAnnotation VariantAnnotation BSgenome
updated 10.8 years ago by ▴ 20 • written 10.8 years ago by ▴ 50
4
votes
4
replies
1.7k
views
readVcfAsVRanges + FilterRules
variantannotation filterVcf readvcfasvranges filterRules
updated 8.0 years ago by 25k • written 8.0 years ago by ▴ 50
2
votes
3
replies
584
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
0
votes
21
replies
3.1k
views
VariantAnnotation Errors and void outputs
variantannotation readvcf
7.7 years ago pifferdavide • 0
0
votes
3
replies
788
views
Bioconductor refLocs2TranscriptLocs function
VariantAnnotation convert GenomicRanges VariantAnnotation VariantAnnotation convert
9.4 years ago Michael Lawrence 11k
7
votes
3
replies
821
views
Extracting first member of each element of a matrix of lists
variantannotation vcf
updated 7.8 years ago by 11k • written 7.8 years ago by 21k
4
votes
10
replies
2.1k
views
Best way to import from multiple VCF files?
variantannotation
updated 6.5 years ago by 3.4k • written 6.5 years ago by ▴ 150
0
votes
7
replies
2.2k
views
VariantAnnotation: Performance and memory issues in readVcf
VariantAnnotation PROcess Rsamtools VariantAnnotation VariantAnnotation PROcess Rsamtools
updated 9.7 years ago by 6.6k • written 9.7 years ago by ▴ 290
0
votes
4
replies
1.1k
views
Finding coding SNPs with predictCoding
SNP VariantAnnotation BSgenome SNPlocs BSgenome VariantAnnotation SNP VariantAnnotation
updated 11.0 years ago by ★ 6.7k • written 11.0 years ago by ▴ 650
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
1
vote
7
replies
2.1k
views
Data from ##SAMPLE lines in VCF?
variantannotation coldata
updated 4.4 years ago by ★ 6.7k • written 4.4 years ago by ▴ 10
0
votes
8
replies
2.2k
views
Best practices to find intersection among variants
VariantAnnotation genomes VariantAnnotation VariantAnnotation genomes VariantAnnotation
updated 8.5 years ago by ★ 1.3k • written 8.5 years ago by ▴ 220
3
votes
5
replies
1.1k
views
filterVcf: crash with isSNV() filter argument
VariantAnnotation filterVcf
7.5 years ago pau.puigdevall • 0
1
vote
2
replies
707
views
VariantAnnotation CollapsedVCF trouble
variantannotation subsetting
6.4 years ago Fabian Grammes ▴ 20
2
votes
2
replies
959
views
readVCFAsVRanges in VariantAnnotation broken by an FTZ format?
variantannotation readvcfasvranges vcf
updated 6.5 years ago by 11k • written 6.5 years ago by ▴ 120
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
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
2
votes
3
replies
1.1k
views
predictCoding fails with error
VariantAnnotation
6.4 years ago • updated 6.3 years ago Stephane Plaisance | VIB | ▴ 60
2
votes
4
replies
1.3k
views
Best way to create a VRanges object from a large VCF file?
variantannotation readvcf readvcfasvranges vcf
updated 6.1 years ago by 11k • written 6.1 years ago by • 0
0
votes
20
replies
1.8k
views
VariantAnnotation function getTranscriptSeqs() gives error "object '.makeUCSCTxListFromGRangesList' not found"
variantannotation
7.5 years ago • updated 7.3 years ago Tjeerd Dijkstra • 0
0
votes
4
replies
1.7k
views
'namespace:Biostrings' error when installing VariantAnnotation
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
updated 9.6 years ago by 13k • written 9.6 years ago by ▴ 20
0
votes
4
replies
1.3k
views
VariantAnnotation: scanVcfHeader() throws error about missing keepNA
VariantAnnotation readVcfHeader
7.6 years ago dan.gatti • 0
0
votes
2
replies
1.2k
views
DNAStringSet_translate error in predictCoding()
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
updated 8.6 years ago by ★ 6.7k • written 8.6 years ago by ▴ 20
0
votes
3
replies
784
views
VariantAnnotation dbSNPs strand
variantannotation
6.8 years ago ribioinfo ▴ 100
3
votes
4
replies
1.0k
views
No annotation for single SNPs
variantannotation SNPs txdb.hsapiens.ucsc.hg19.knowngene ucsc
updated 5.6 years ago by ★ 6.7k • written 5.6 years ago by • 0
2
votes
3
replies
1.7k
views
Metadata Missing from vcf when reading in with readVcfAsVRanges
variantannotation vranges readvcf readvcfasvranges metadata
8.0 years ago summerela • 0
2
votes
2
replies
2.1k
views
Vranges (somatic signature) VariantAnnotation
software error variantannotation
updated 8.3 years ago by 13k • written 8.3 years ago by • 0
3
votes
6
replies
1.4k
views
VariantAnnotation non-model species
variantannotation
8.0 years ago Miss Agnieszka Aleksandra Golicz ▴ 40
0
votes
5
replies
1.6k
views
VariantAnnotation _ problem in merging files, mutationspectrum per sample
variantannotation
updated 8.2 years ago by ★ 1.3k • written 8.2 years ago by • 0
0
votes
2
replies
1.9k
views
VariantAnnotation Installation Error RSQLite
VariantAnnotation RSQLite
8.2 years ago remi.tournebize ▴ 10
1
vote
4
replies
5.0k
views
merging VCF files
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
written 10.0 years ago by ★ 6.7k
3
votes
2
replies
984
views
VariantAnnotation package, subseting vcfs on fixed fields
variantannotation vcf fixed filter
8.1 years ago Anna N. • 0
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
1
vote
2
replies
1.1k
views
Rsamtools and dbnsfp
bioconductor rsamtools annotation variantannotation
7.6 years ago jhomsy • 0
0
votes
2
replies
1.9k
views
merging VCF files
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
written 10.1 years ago by ▴ 840
0
votes
2
replies
1.5k
views
Error in locateVariants
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
updated 9.5 years ago by ★ 6.7k • written 9.5 years ago by ▴ 10
0
votes
2
replies
987
views
Problem with VariantAnnotation and VCF "R" genotype fields when expanding CollapsedVCF
VariantAnnotation bug
updated 6.2 years ago by ★ 6.7k • written 6.2 years ago by 21k
0
votes
2
replies
1.1k
views
VariantAnnotation ALT Field
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
updated 10.2 years ago by ▴ 750 • written 10.2 years ago by ▴ 60
2
votes
3
replies
1.0k
views
readVcf skipping CS field in INFO
variantannotation readVcf
updated 8.3 years ago by ★ 6.7k • written 8.3 years ago by ▴ 630
0
votes
5
replies
1.4k
views
VariantAnnotation and distance to genes
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
updated 9.7 years ago by 62k • written 9.7 years ago by ▴ 20
0
votes
2
replies
2.7k
views
Problem reading VCF file using readVcf from package VariantAnnotation
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
updated 9.8 years ago by ★ 6.7k • written 9.8 years ago by ▴ 290
4
votes
3
replies
1.2k
views
how to save file on local disk after applying predictCoding() function?
vcf predict coding save file VariantAnnotation
updated 8.3 years ago by ▴ 80 • written 8.3 years ago by ▴ 10
0
votes
3
replies
1.0k
views
writeVcf bug
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
updated 9.8 years ago by ★ 6.7k • written 9.8 years ago by ▴ 60
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Comment: Strand information in a GAlignmentsList object derived from strand-specific pair by Hervé Pagès 16k
Got it. Yeah I guess having a `strandMode` parameter for `readGAlignmentsList()` would help handle this. @Robert: Do you want to open an i…
Comment: Strand information in a GAlignmentsList object derived from strand-specific pair by James W. MacDonald 62k
One reason to use a GAlignmentsList object is if you have 'too many' unpaired reads for some reason and you want to recover them. And it's …
Comment: Strand information in a GAlignmentsList object derived from strand-specific pair by Hervé Pagès 16k
Hi Robert, Just to clarify, a GAlignmentsList object represents a list of GAlignments objects, in the same way that a GRangesList object r…
Comment: AnnotationForge::makeOrgPackageFromNCBI - ERROR to access url (NCBI FTP site) by James W. MacDonald 62k
Does this work? ``` > tmp <- tempfile("whatevs") > download.file("ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2pubmed.gz", tmp, mode = "wb") …
Comment: Not able to download recount3 data by Niveditha ▴ 10
Thank you so much, Leo. This works.
Votes
Comment: STRINGdb string_db$map error
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
Answer: Library sizes of miRNA sequencing data and TMM normalization with Edge-R
C: Can't install TopmedPipeline Package
Comment: Question about GWASTools gdsSubset
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