Showing : variantAnnotation • reset
3
votes
3
replies
1.8k
views
makeVRangesFromGRanges throws coercing "factor" to "NA" error
r packages somaticsignatures variantannotation
updated 9.5 years ago by 25k • written 9.5 years ago by ▴ 10
0
votes
2
replies
1.3k
views
vcf intersection variantannotation
variantannotation
updated 9.5 years ago by ★ 11k • written 9.5 years ago by ▴ 100
0
votes
1
reply
924
views
Bug in VRanges conversion in VariantAnnotation (devel)
VariantAnnotation
updated 9.5 years ago by ★ 11k • written 9.5 years ago by • 0
1
vote
1
reply
985
views
VariantAnnotation quality filter
variantannotation
9.5 years ago ribioinfo ▴ 100
0
votes
2
replies
2.1k
views
Subsetting info columns from a VCF and getting rsID for some row names?
R variantannotation vcf scanvcfparam readvcf
updated 9.5 years ago by ★ 11k • written 9.5 years ago by • 0
0
votes
1
reply
822
views
modified the header data in the fixed slots of a VCFHeader object
variantannotation
updated 9.6 years ago by ★ 11k • written 9.6 years ago by • 0
4
votes
5
replies
1.8k
views
parRapply in BiocParallel ?
biocparallel variantannotation
updated 9.6 years ago by ★ 11k • written 9.6 years ago by ▴ 350
0
votes
1
reply
1.2k
views
[VariantAnnotation] Unable to set a genotype with geno()
variantannotation
updated 9.6 years ago by 4.2k • written 9.6 years ago by • 0
0
votes
3
replies
1.4k
views
VariantAnnotation dbSNPs strand
variantannotation
9.7 years ago ribioinfo ▴ 100
1
vote
1
reply
1.4k
views
Building VariantAnnotation on Windows - Makevars.win error
windows variantannotation makevars.win
updated 9.7 years ago by 25k • written 9.7 years ago by ▴ 10
0
votes
2
replies
2.0k
views
Duplicated rows in readVcf output
variantannotation readvcf
updated 9.7 years ago by ★ 6.8k • written 9.7 years ago by • 0
0
votes
7
replies
2.3k
views
VariantAnnotation produces duplicate names
variantannotation
updated 9.7 years ago by ★ 6.8k • written 9.7 years ago by ▴ 40
2
votes
1
reply
1.9k
views
VariantAnnotation as.vranges with asterisk in ALT field
variantannotation gatk
updated 9.7 years ago by ★ 11k • written 9.7 years ago by ▴ 70
0
votes
2
replies
2.1k
views
Gene symbol annotation not converted for intergenic SNPs with multiple genes
annotation variantannotation rstudio
updated 9.8 years ago by ★ 6.8k • written 9.8 years ago by • 0
4
votes
4
replies
2.3k
views
filterVcf by sample id
variantannotation
updated 9.8 years ago by ★ 6.8k • written 9.8 years ago by ▴ 470
5
votes
6
replies
4.1k
views
Error in reading 1000 genomes data
variantannotation
updated 9.8 years ago by 25k • written 11.1 years ago by ▴ 20
0
votes
1
reply
1.7k
views
Subsetting the geno fields in a VCF using VariantAnnotation
VariantAnnotation
updated 9.8 years ago by ★ 11k • written 9.8 years ago by ▴ 110
0
votes
2
replies
2.1k
views
readVcf error: Call2("new_XStringSet_from_CHARACTER", ans_class, ans_elementType, : key 42 (char '*') not in lookup table
VariantAnnotation
9.8 years ago rubi ▴ 110
0
votes
1
reply
4.3k
views
Subset VCF files using multiple criteria
vcf variantannotation granges
9.9 years ago georgewwp • 0
0
votes
3
replies
2.7k
views
vcf postion extract
vcf variantannotation position
updated 9.9 years ago by 25k • written 9.9 years ago by • 0
1
vote
1
reply
1.2k
views
Effieicntly convert DNAStringSetList to a character vector
variantannotation
10.0 years ago dr ▴ 10
1
vote
1
reply
2.0k
views
Write the "map" DataFrame from genotypeToSnpMatrix() to a text file
variantannotation DataFrame snpstats
10.1 years ago TimothéeFlutre ▴ 80
2
votes
5
replies
3.2k
views
Plot data from VCF using Gviz?
gviz variantannotation vcf
updated 10.1 years ago by ★ 6.8k • written 10.1 years ago by ★ 2.1k
2
votes
3
replies
1.6k
views
genotypeToSnpMatrix doesn't handle PL
variantannotation vcf
updated 10.1 years ago by ▴ 890 • written 10.2 years ago by ▴ 80
1
vote
1
reply
1.2k
views
inconsistent default of file suffix
variantannotation rsamtools
updated 10.1 years ago by ★ 6.8k • written 10.1 years ago by ▴ 80
0
votes
2
replies
1.6k
views
motifbreakR VariantAnnotation namespace error on reading vcf file
motifbreakR variantannotation
updated 10.1 years ago by ▴ 50 • written 10.1 years ago by ▴ 20
2
votes
1
reply
1.6k
views
Error in extractROWS(x, eval(filter, x))
variantannotation filtervcf
updated 10.1 years ago by ★ 11k • written 10.1 years ago by ▴ 80
1
vote
2
replies
1.5k
views
Error: could not find function "PartitioningByEnd"
variantannotation iranges
updated 10.1 years ago by ★ 11k • written 10.1 years ago by ▴ 80
0
votes
7
replies
3.8k
views
append to bgzipped VCF file
variantannotation tabix
updated 10.1 years ago by ★ 11k • written 10.1 years ago by ▴ 80
2
votes
2
replies
1.8k
views
a filter works alone but not with other filters
variantannotation vcf filtervcf
updated 10.2 years ago by 25k • written 10.2 years ago by ▴ 80
5
votes
2
replies
1.5k
views
filter "isSnp" for VCF
variantannotation filtervcf vcf
updated 10.2 years ago by ★ 11k • written 10.2 years ago by ▴ 80
0
votes
20
replies
3.3k
views
VariantAnnotation function getTranscriptSeqs() gives error "object '.makeUCSCTxListFromGRangesList' not found"
variantannotation
10.4 years ago • updated 10.2 years ago Tjeerd Dijkstra • 0
0
votes
4
replies
2.0k
views
readVcf error resulting from star * in alt allele field
variantannotation
updated 10.2 years ago by ★ 6.8k • written 10.2 years ago by ▴ 170
0
votes
1
reply
1.6k
views
library(VariantAnnotation) download difficulties
variantannotation
updated 10.3 years ago by ★ 6.8k • written 10.3 years ago by • 0
1
vote
4
replies
2.7k
views
variantAnnotation::locateVariants() with AllVariants(): why do some input variants not get annotated?
variantannotation locatevariants
10.3 years ago Jakob Goldmann • 0
0
votes
2
replies
1.4k
views
predictCoding with multiple samples
predict coding variantannotation
updated 10.3 years ago by ★ 6.8k • written 10.3 years ago by • 0
1
vote
2
replies
5.7k
views
ICU init failed: U_FILE_ACCESS_ERROR while loading library "VariantAnnotation"
variantannotation library error
updated 10.3 years ago by ★ 6.8k • written 10.3 years ago by ▴ 50
0
votes
2
replies
1.9k
views
filterVcf: error with param argument
VariantAnnotation filterVcf ScanVcfParam vcf writeVcf
updated 10.4 years ago by 25k • written 10.4 years ago by • 0
3
votes
5
replies
2.0k
views
filterVcf: crash with isSNV() filter argument
VariantAnnotation filterVcf
10.4 years ago pau.puigdevall • 0
1
vote
8
replies
1.8k
views
writeVCF outputs invalid VCF if no genotypes
variantannotation
updated 10.4 years ago by ★ 6.8k • written 10.4 years ago by ▴ 40
2
votes
4
replies
2.4k
views
customProDB: error aberrant fasta from indels
indel customprodb fasta variantannotation
updated 10.5 years ago by ▴ 50 • written 10.5 years ago by • 0
1
vote
2
replies
1.7k
views
Rsamtools and dbnsfp
bioconductor rsamtools annotation variantannotation
10.5 years ago jhomsy • 0
0
votes
4
replies
2.1k
views
VariantAnnotation: scanVcfHeader() throws error about missing keepNA
VariantAnnotation readVcfHeader
10.5 years ago dan.gatti • 0
0
votes
1
reply
1.6k
views
trouble with predictCoding( function
snp variantannotation predict coding
10.5 years ago vakul.mohanty ▴ 20
0
votes
6
replies
3.7k
views
readVcf shape of 'skeleton' is not compatible with 'NROW(flesh)'
variantannotation
updated 10.5 years ago by ★ 6.8k • written 10.5 years ago by ▴ 40
2
votes
3
replies
2.0k
views
locateVariants with sample names
annotation variantannotation sample
10.6 years ago by0 • 0
2
votes
9
replies
3.8k
views
ReadVCF not reading samples
readvcf vcf variantannotation
10.6 years ago askates ▴ 10
0
votes
21
replies
5.8k
views
VariantAnnotation Errors and void outputs
variantannotation readvcf
10.6 years ago pifferdavide • 0
7
votes
3
replies
1.6k
views
Extracting first member of each element of a matrix of lists
variantannotation vcf
updated 10.6 years ago by ★ 11k • written 10.6 years ago by 21k
1
vote
5
replies
5.2k
views
Converting a DNAStringSetList to characters quickly
readVcf DNAStringSet DNAStringSetList variantannotation readvcf
10.7 years ago dan.gatti • 0
217 results • Page 3 of 5
Recent ...
Replies
Answer: segfault in edgeR glmQLFit by Gordon Smyth 53k
Dear Mark, Thank you for providing a reproducible example. I confirm that I can reproduce the segfault myself on my own computer. We will …
Answer: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink by aqeel • 0
Discover the pinnacle of Brazilian Jiu Jitsu gear at [Dragon][1] GI. [1]: https://dragongi.com/
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by Gordon Smyth 53k
I refered you to the DiffVar package 11 months ago. Did you consider it? Your clarification makes it clear that your issue is not with lim…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by jtsy6383 • 0
Thanks for the reply Gordon. I am also working on the project and have been tasked to reformulate and add some details. We're interested i…
Answer: How does contrasts.fit do in limma to extract comparisons with a model having in by Gordon Smyth 53k
The limma Users Guide explains how to test for interactions or to test for contrasts very easily. limma can work with any design matrix, bu…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Awards • All
Popular Question to Vincent J. Carey, Jr. 6.7k
Popular Question to Istvan Albert ▴ 50
Popular Question to Dario Strbenac ★ 1.6k
Scholar to Nikos Ignatiadis ▴ 180
Popular Question to Robert • 0
Locations • All
The city by the bay, 17 minutes ago
United States, 1 hour ago
WEHI, Melbourne, Australia, 5 hours ago
Hong Kong, 6 hours ago
Pakistan, 6 hours ago
Traffic: 1564 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6