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variantannotation
•
reset
0
votes
2
replies
158
views
VariantAnnotation not does escape = within header string quotes
VariantAnnotation
updated 5 weeks ago by
Kevin Blighe
★ 4.0k • written 5 weeks ago by
Daniel Cameron
▴ 40
0
votes
1
reply
392
views
Problem using locateVariants() from the VariantAnnotation package
VariantAnnotation
vari
9 months ago
Marco
• 0
0
votes
1
reply
628
views
ensemblVEP deprecation and how to reproduce
VariantAnnotation
updated 15 months ago by
Vincent J. Carey, Jr.
6.7k • written 15 months ago by
kmzhou4
• 0
0
votes
0
replies
667
views
Using variantAnnotation to put together genotype and consequence information
variantAnn
VariantAnnotation
17 months ago
ramiro.barrantes
▴ 10
1
vote
2
replies
2.0k
views
How to compare subset of samples from VCF files
VCF
VariantAnnotation
updated 18 months ago by
Gordon Smyth
53k • written 18 months ago by
Marco
• 0
0
votes
0
replies
605
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
20 months ago
Stevie Pederson
• 0
2
votes
1
reply
755
views
Is random access by row index possible for an indexed VCF file?
Rsamtools
VariantAnnotation
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
maltethodberg
▴ 180
0
votes
0
replies
549
views
RFC: significant changes to ensemblVEP package
VariantAnnotation
ensemblVEP
23 months ago
Vincent J. Carey, Jr.
6.7k
0
votes
5
replies
1.2k
views
locateVariant from VariantAnnotation returns wrong results
VariantAnnotation
locateVariant
updated 2.0 years ago by
James W. MacDonald
68k • written 2.1 years ago by
nhaus
▴ 70
0
votes
0
replies
1.3k
views
Variant Filtering on very large VCF files
VariantAnnotation
VariantFiltering
2.2 years ago
Bogdan
▴ 670
2
votes
2
replies
2.1k
views
Matching Variants Between Two VCF Objects
VariantAnnotation
written 5.1 years ago by
Dario Strbenac
★ 1.6k
0
votes
2
replies
1.2k
views
Docker usage with Trio Bioconductor Package
VariantAnnotation
docker
trio
updated 2.6 years ago by
ATpoint
★ 5.0k • written 2.6 years ago by
sethberke
• 0
4
votes
8
replies
3.0k
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
2.8 years ago • updated 2.7 years ago
davidhillis
• 0
0
votes
0
replies
979
views
VariantAnnotation::readVcf incorrectly processes GATK Mutect2 vcf INFO field AS_SB_TABLE
vcf
AS_SB_TABLE
readVcf
Mutect2
VariantAnnotation
2.8 years ago
therealgenna
• 0
0
votes
3
replies
2.0k
views
Add GP values to VCF
VariantAnnotation
2.9 years ago
Stephanie M. Gogarten
▴ 890
0
votes
1
reply
2.9k
views
Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123
VariantFiltering
Alignment
VariantAnnotation
updated 3.1 years ago by
James W. MacDonald
68k • written 3.1 years ago by
Mohamed
▴ 30
2
votes
4
replies
1.7k
views
Error message from protein coding prediction with VariantAnnotation
R
VariantAnnotation
3.3 years ago
rwan.work
• 0
0
votes
2
replies
1.3k
views
Error message from protein coding prediction with VariantAnnotation
R
VariantAnnotation
3.3 years ago
rwan.work
• 0
0
votes
2
replies
3.3k
views
merging VCF files
VariantAnnotation
VariantAnnotation
VariantAnnotation
VariantAnnotation
written 12.9 years ago by
Stephanie M. Gogarten
▴ 890
0
votes
3
replies
1.6k
views
Problem with intronic variants in VariantAnnotation
VariantAnnotation
updated 3.8 years ago by
Raül
• 0 • written 4.0 years ago by
paolo.provero
• 0
0
votes
2
replies
1.8k
views
Reading vcf file with readVcf
VariantAnnotation
4.2 years ago
aurelien.dejode
• 0
0
votes
2
replies
1.3k
views
Multiple exons for predictCoding() from VariantAnnotation (use phase information from gff3 file)?
VariantAnnotation
updated 4.3 years ago by
Hervé Pagès
16k • written 4.4 years ago by
Kasper_holm2
• 0
0
votes
5
replies
2.2k
views
installation error: Error in setIs(class2, cli, extensionObject = obji, doComplete = FALSE and setClass() for chromVAR and VariantAnnotation
Install
VariantAnnotation
Bioconductor
chromVAR
updated 4.3 years ago by
Vincent J. Carey, Jr.
6.7k • written 4.3 years ago by
Hannah
• 0
0
votes
1
reply
1.4k
views
GRanges object out-of-bound
VariantAnnotation
updated 4.3 years ago by
Vincent J. Carey, Jr.
6.7k • written 4.4 years ago by
Kasper_holm2
• 0
2
votes
3
replies
1.6k
views
readVcf(remoteFile, "hg19", "region") works on macos, fails on linux and in docker
open.BcfFile
VariantAnnotation
updated 23 months ago by
Alex
• 0 • written 4.4 years ago by
Paul Shannon
▴ 470
0
votes
0
replies
916
views
Annotate mutations on DNA level to splice transcripts
VariantAnnotation
4.4 years ago
Kasper_holm2
• 0
0
votes
4
replies
2.6k
views
Error of read in large vcf file using readVcf
SomaticSignatures
VariantAnnotation
updated 4.5 years ago by
James W. MacDonald
68k • written 4.5 years ago by
xiw588
• 0
0
votes
2
replies
1.8k
views
VariantAnnotation::readVcf not reading variants
VariantAnnotation
updated 4.6 years ago by
James W. MacDonald
68k • written 4.6 years ago by
peiwen.li
• 0
0
votes
2
replies
3.4k
views
VCF File too large for tabix. Best option to make it usable with R?
samtools
tabix
VariantAnnotation
VCFArray
updated 4.7 years ago by
Vincent J. Carey, Jr.
6.7k • written 4.8 years ago by
naive
• 0
1
vote
12
replies
4.8k
views
readVcf does not recognize tabix index
VariantAnnotation
readvcf
tabix
updated 4.7 years ago by
Vincent J. Carey, Jr.
6.7k • written 4.8 years ago by
naive
• 0
0
votes
2
replies
2.1k
views
readVCF requires the argument "genome". What does it stand for?
Genome
readVcf
VariantAnnotation
4.8 years ago
naive
• 0
2
votes
4
replies
2.1k
views
Obtaining Comments From VCF Header
VariantAnnotation
VCFHeader
written 5.5 years ago by
Dario Strbenac
★ 1.6k
3
votes
2
replies
2.0k
views
Import or Subset VCF PASS Variants
VariantAnnotation
subset
ScanVcfParam
updated 5.7 years ago by
Martin Morgan
25k • written 5.7 years ago by
Dario Strbenac
★ 1.6k
0
votes
2
replies
1.8k
views
Extract structural variant and flanking sequence from VCF and fasta, in R
VariantAnnotation
Bioconductor
VCF
Structural variants
R
updated 5.7 years ago by
Martin Morgan
25k • written 5.7 years ago by
W. van Rengs
• 0
0
votes
1
reply
1.0k
views
Can strand be set to minus in VRanges objects?
VariantAnnotation
updated 5.9 years ago by
James W. MacDonald
68k • written 5.9 years ago by
david.mas
• 0
0
votes
1
reply
1.8k
views
FilterVCF Filter '' failed: shape of 'skeleton' is not compatible with 'NROW(flesh)'
variantAnnotation
updated 6.2 years ago by
Martin Morgan
25k • written 6.2 years ago by
b.curran
• 0
2
votes
3
replies
2.2k
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 6.4 years ago by
Steve Lianoglou
★ 13k • written 6.4 years ago by
james.dalgleish
▴ 30
2
votes
3
replies
1.6k
views
VariantAnnotation - subset multi-allele variants
variantAnnotation
updated 6.4 years ago by
Michael Lawrence
★ 11k • written 6.4 years ago by
user1986
• 0
0
votes
1
reply
1.2k
views
negative AD value interfering with readVcfasVRanges
VariantAnnotation
updated 6.5 years ago by
Michael Lawrence
★ 11k • written 6.5 years ago by
TRASA
• 0
0
votes
3
replies
1.5k
views
rbind VCF Two Objects Column Names Error
VariantAnnotation
VCF
6.5 years ago
Dario Strbenac
★ 1.6k
0
votes
0
replies
1.2k
views
predictCoding warning message: serious or not?
software error
annotation
VariantAnnotation
updated 6.7 years ago by
shepherl
4.2k • written 6.7 years ago by
longsong
• 0
2
votes
3
replies
2.2k
views
Error in VCF parsing with VariantAnnotation
software error
VariantAnnotation
ensemblVEP
updated 6.8 years ago by
Valerie Obenchain
★ 6.8k • written 6.8 years ago by
mumichae
▴ 20
4
votes
9
replies
4.6k
views
Create protein sequences including variants from a VCF file
VariantAnnotation
customProDB
updated 19 months ago by
Yun
• 0 • written 6.8 years ago by
daniel.magnus.bader
▴ 50
0
votes
1
reply
1.3k
views
VariantAnnotation fails to load VCF record
variantannotation
7.0 years ago
Daniel Cameron
▴ 40
0
votes
6
replies
2.3k
views
How to prepare .vcf for seqCAT
seqCAT
variantannotation
gatk
updated 7.0 years ago by
erikfas
▴ 30 • written 7.1 years ago by
abe
• 0
0
votes
1
reply
1.3k
views
writeVcf save invalid vcf with metadata out of order
variantannotation
updated 7.1 years ago by
Valerie Obenchain
★ 6.8k • written 7.1 years ago by
alessandro.pastore
▴ 20
1
vote
7
replies
4.3k
views
Data from ##SAMPLE lines in VCF?
variantannotation
coldata
updated 7.2 years ago by
Valerie Obenchain
★ 6.8k • written 7.2 years ago by
lvclark
▴ 10
3
votes
3
replies
1.8k
views
Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
variantannotation
updated 7.5 years ago by
Valerie Obenchain
★ 6.8k • written 7.5 years ago by
goldberg.jm
▴ 10
3
votes
4
replies
2.4k
views
Problem when transforming Platypus vcf to VRanges
variantannotation
vcf
readvcf
vranges
updated 7.5 years ago by
Michael Lawrence
★ 11k • written 7.5 years ago by
david.mas
• 0
0
votes
2
replies
1.7k
views
Error: invalid class "VRanges" object
variantannotation
VRanges
R
Rle
updated 7.5 years ago by
Valerie Obenchain
★ 6.8k • written 7.5 years ago by
Jayendra Shinde
• 0
217 results • Page
1 of 5
Recent ...
Replies
Answer: NUPOP usage
by
shepherl
4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker?
by
fnfgame
• 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes
by
Erik Wright
▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
by
Michael Love
43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup.Maybe give the traceb…
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
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