Showing : variantAnnotation • reset
1
vote
10
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3.2k
views
predictCoding error DNAStringSet_translate
variantannotation predict coding
updated 10.6 years ago by ★ 6.8k • written 10.6 years ago by ▴ 40
0
votes
5
replies
2.5k
views
Error installing VariantAnnotation with bioconductor/devel_core
install variantannotation
10.6 years ago kforner • 0
4
votes
4
replies
2.6k
views
readVcfAsVRanges + FilterRules
variantannotation filterVcf readvcfasvranges filterRules
updated 10.7 years ago by 25k • written 10.7 years ago by ▴ 50
2
votes
3
replies
2.9k
views
Metadata Missing from vcf when reading in with readVcfAsVRanges
variantannotation vranges readvcf readvcfasvranges metadata
10.7 years ago summerela • 0
3
votes
5
replies
3.9k
views
Add Custom Annotations to Multi-Sample VCF with VariantAnnotation() package
variantannotation granges DNAStringSetList findoverlaps Vranges
10.7 years ago summerela • 0
4
votes
6
replies
2.4k
views
VariantAnnotation non-model species
variantannotation
10.7 years ago Miss Agnieszka Aleksandra Golicz ▴ 40
3
votes
2
replies
1.6k
views
VariantAnnotation package, subseting vcfs on fixed fields
variantannotation vcf fixed filter
10.8 years ago Anna N. • 0
2
votes
2
replies
1.7k
views
promoter definition in VariantAnnotation
VariantAnnotation promoter drosophila melanogaster
updated 10.8 years ago by ★ 6.8k • written 10.8 years ago by ▴ 30
4
votes
11
replies
2.6k
views
Filter every X position
variantannotation
10.9 years ago • updated 10.8 years ago remi.tournebize ▴ 10
0
votes
5
replies
2.6k
views
VariantAnnotation _ problem in merging files, mutationspectrum per sample
variantannotation
updated 10.9 years ago by ★ 1.3k • written 10.9 years ago by • 0
2
votes
4
replies
2.2k
views
Memory usage in readVcf from VariantAnnotation
VariantAnnotation
10.9 years ago Kasper Daniel Hansen ★ 6.5k
1
vote
12
replies
3.4k
views
VariantAnnotation: no method for function 'path' for signature 'character'
variantannotation readvcf readgt
updated 10.9 years ago by ★ 6.8k • written 10.9 years ago by ▴ 150
0
votes
1
reply
1.8k
views
readVCF (VariantAnnotation) problem with mismatched header and info fields in vcf file
annotation vcf readvcf variantannotation
10.9 years ago jls2282 • 0
0
votes
2
replies
1.6k
views
How to correct VCF Iranges from width=1 to correct end coordinate
VCF iranges End software error variantannotation
10.9 years ago tiffanie.moss • 0
0
votes
2
replies
2.7k
views
VariantAnnotation Installation Error RSQLite
VariantAnnotation RSQLite
10.9 years ago remi.tournebize ▴ 10
3
votes
4
replies
4.4k
views
Quality filtering of exactSNP-generated VCF files
exactSNP qc variantannotation
updated 10.9 years ago by ★ 3.6k • written 11.0 years ago by ▴ 100
0
votes
10
replies
3.6k
views
Incorrect row names when a VCF has multiple ALTs.
variantannotation vcf
updated 11.0 years ago by ★ 6.8k • written 11.0 years ago by • 0
7
votes
5
replies
1.6k
views
writeVcf no longer writes records for ungenotyped data
variantannotation
updated 11.0 years ago by ★ 6.8k • written 11.0 years ago by ▴ 40
2
votes
3
replies
1.6k
views
readVcf skipping CS field in INFO
variantannotation readVcf
updated 11.0 years ago by ★ 6.8k • written 11.0 years ago by ▴ 760
0
votes
5
replies
2.2k
views
VariantAnnotation VCF read error
variantannotation readvcf
updated 11.0 years ago by ★ 6.8k • written 11.0 years ago by ▴ 10
2
votes
6
replies
3.9k
views
Import of vcf with VariantAnnotation
variantannotation somaticsignatures
11.0 years ago Anna N. • 0
3
votes
2
replies
5.4k
views
Add data to Vcf Info Field
variantannotation
updated 11.0 years ago by ★ 6.8k • written 11.0 years ago by ▴ 50
0
votes
1
reply
1.4k
views
predictCoding function in VariantAnnotation packages
variantannotation
updated 11.0 years ago by ★ 6.8k • written 11.0 years ago by • 0
2
votes
2
replies
2.8k
views
Vranges (somatic signature) VariantAnnotation
software error variantannotation
updated 11.0 years ago by ★ 13k • written 11.0 years ago by • 0
4
votes
3
replies
1.9k
views
how to save file on local disk after applying predictCoding() function?
vcf predict coding save file VariantAnnotation
updated 11.0 years ago by ▴ 90 • written 11.1 years ago by ▴ 10
2
votes
1
reply
2.2k
views
'seqlevels(seqinfo(x))' and 'levels(seqnames(x))' are not identical
variantannotation seqlevels error
updated 11.1 years ago by ★ 6.8k • written 11.1 years ago by ▴ 290
0
votes
8
replies
3.5k
views
Best practices to find intersection among variants
VariantAnnotation genomes VariantAnnotation VariantAnnotation genomes VariantAnnotation
updated 11.2 years ago by ★ 1.3k • written 11.2 years ago by ▴ 220
0
votes
0
replies
1.1k
views
Complete variant toolbox: gmapR/VariantTools/VariantAnnotation - revived
VariantAnnotation Annotation GenomicRanges VariantAnnotation GenomicAlignments Annotation
11.2 years ago Valerie Obenchain ★ 6.8k
0
votes
5
replies
1.6k
views
Complete variant toolbox: gmapR/VariantTools/VariantAnnotation - revived
VariantAnnotation GenomicRanges VariantAnnotation VariantAnnotation GenomicRanges
updated 11.2 years ago by ★ 3.4k • written 11.3 years ago by ★ 6.8k
0
votes
2
replies
1.6k
views
DNAStringSet_translate error in predictCoding()
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
updated 11.3 years ago by ★ 6.8k • written 11.4 years ago by ▴ 20
0
votes
7
replies
2.1k
views
mutant allele read counts
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
updated 11.4 years ago by ★ 6.8k • written 11.4 years ago by ★ 13k
0
votes
1
reply
2.8k
views
help with analysis of genotyping data from Illumina HumanOmni5-4v1_B chip
SNP VariantAnnotation Annotation probe VariantAnnotation GWASTools SNP VariantAnnotation
updated 11.4 years ago by ▴ 890 • written 11.4 years ago by ▴ 160
0
votes
1
reply
4.0k
views
Multi-sample VCF file and filterVcf
VariantAnnotation Annotation VariantAnnotation VariantAnnotation Annotation VariantAnnotation
updated 11.4 years ago by ★ 6.8k • written 11.4 years ago by ★ 13k
0
votes
3
replies
1.5k
views
VariantAnnotation - extracting AD and PL fields
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
updated 11.5 years ago by ★ 11k • written 11.5 years ago by ▴ 20
0
votes
2
replies
4.4k
views
VariantAnnotation R Package - Merging Two VCF files
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
written 11.7 years ago by ▴ 320
0
votes
9
replies
2.6k
views
variantAnnotation: alternative GENETIC_CODE, and circular chromosomes?
VariantAnnotation Cancer Yeast annotate Biostrings VariantAnnotation VariantAnnotation
updated 11.7 years ago by 16k • written 11.7 years ago by ▴ 740
0
votes
5
replies
2.5k
views
Complete variant toolbox: gmapR/VariantTools/VariantAnnotation
BiocViews VariantAnnotation Annotation biocViews Rsubread VariantAnnotation gmapR BiocViews
11.9 years ago • updated 11.8 years ago Thomas Girke ★ 1.7k
0
votes
11
replies
2.8k
views
Complete variant toolbox: gmapR/VariantTools/VariantAnnotation
VariantAnnotation Annotation VariantAnnotation VariantTools VariantAnnotation Annotation
updated 11.9 years ago by ★ 6.8k • written 11.9 years ago by ★ 1.7k
0
votes
0
replies
1.6k
views
zero-row result breaks select() on PolyPhen.Hsapiens.* and SIFT.Hsapiens.*
VariantAnnotation Annotation PolyPhen SIFT annotate VariantAnnotation ensemblVEP Annotation
11.9 years ago Valerie Obenchain ★ 6.8k
0
votes
2
replies
1.3k
views
readVcf fails when ALT field contains breakends and no symbolic allele
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
updated 12.0 years ago by ▴ 40 • written 12.0 years ago by ★ 6.8k
0
votes
2
replies
1.3k
views
stranded intronic variants with VariantAnnotation::locateVariants()
VariantAnnotation Annotation VariantAnnotation VariantAnnotation Annotation VariantAnnotation
updated 12.0 years ago by ★ 6.8k • written 12.0 years ago by ★ 3.4k
0
votes
3
replies
1.2k
views
Bioconductor refLocs2TranscriptLocs function
VariantAnnotation convert GenomicRanges VariantAnnotation VariantAnnotation convert
12.1 years ago Michael Lawrence ★ 11k
0
votes
0
replies
969
views
Bioconductor refLocs2TranscriptLocs function
VariantAnnotation convert GenomicRanges VariantAnnotation VariantAnnotation convert
12.1 years ago Michael Lawrence ★ 11k
0
votes
2
replies
1.9k
views
Error in locateVariants
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
updated 12.3 years ago by ★ 6.8k • written 12.3 years ago by ▴ 10
0
votes
4
replies
2.6k
views
'namespace:Biostrings' error when installing VariantAnnotation
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
updated 12.3 years ago by ★ 13k • written 12.3 years ago by ▴ 20
0
votes
7
replies
3.7k
views
VariantAnnotation: Performance and memory issues in readVcf
VariantAnnotation PROcess Rsamtools VariantAnnotation VariantAnnotation PROcess Rsamtools
updated 12.4 years ago by 6.7k • written 12.4 years ago by ▴ 300
0
votes
5
replies
2.1k
views
VariantAnnotation and distance to genes
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
updated 12.4 years ago by 68k • written 12.4 years ago by ▴ 20
0
votes
2
replies
3.6k
views
Problem reading VCF file using readVcf from package VariantAnnotation
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
updated 12.5 years ago by ★ 6.8k • written 12.5 years ago by ▴ 300
0
votes
3
replies
1.5k
views
writeVcf bug
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
updated 12.5 years ago by ★ 6.8k • written 12.5 years ago by ▴ 80
0
votes
0
replies
1.2k
views
Subsetting vcf file by subject
VariantAnnotation Annotation cycle VariantAnnotation VariantAnnotation Annotation cycle
12.5 years ago Valerie Obenchain ★ 6.8k
216 results • Page 4 of 5
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Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
That's weird. Using the example data works for me. ``` > example(read10xCounts) rd10xC> # Mocking up some 10X genomics output. rd10xC> ex…
Comment: Join BOC Sciences at Drug Discovery Chemistry by teamardigen • 0
Sounds like an exciting event for anyone passionate about small molecule innovation. The focus on discovery and optimization really drives …
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
I am, but perhaps I'm not understanding how it should work. > sse = DropletUtils::read10xCounts(curr_files[1], mtx.class = 'SVT_Sparse…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Did you use the development version as Aaron suggested? There is an argument to read the market matrix file directly into an `SVT_SparseMat…
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Drug datasets for RNA-seq
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