Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
variantAnnotation
•
reset
0
votes
0
replies
91
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
22 days ago
Stevie Pederson
• 0
0
votes
1
reply
149
views
Is random access by row index possible for an indexed VCF file?
Rsamtools
VariantAnnotation
updated 7 weeks ago by
James W. MacDonald
65k • written 7 weeks ago by
maltethodberg
▴ 180
2
votes
3
replies
1.1k
views
readVcf(remoteFile, "hg19", "region") works on macos, fails on linux and in docker
open.BcfFile
VariantAnnotation
updated 3 months ago by
Alex
• 0 • written 2.8 years ago by
Paul Shannon
▴ 470
0
votes
0
replies
167
views
RFC: significant changes to ensemblVEP package
VariantAnnotation
ensemblVEP
3 months ago
Vincent J. Carey, Jr.
6.7k
0
votes
5
replies
485
views
locateVariant from VariantAnnotation returns wrong results
VariantAnnotation
locateVariant
updated 5 months ago by
James W. MacDonald
65k • written 5 months ago by
nhaus
▴ 30
0
votes
0
replies
454
views
Variant Filtering on very large VCF files
VariantAnnotation
VariantFiltering
7 months ago
Bogdan
▴ 670
2
votes
2
replies
1.5k
views
Matching Variants Between Two VCF Objects
VariantAnnotation
written 3.4 years ago by
Dario Strbenac
★ 1.5k
0
votes
2
replies
549
views
Docker usage with Trio Bioconductor Package
VariantAnnotation
docker
trio
updated 11 months ago by
ATpoint
★ 4.1k • written 11 months ago by
sethberke
• 0
4
votes
8
replies
1.5k
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
13 months ago
davidhillis
• 0
0
votes
0
replies
478
views
VariantAnnotation::readVcf incorrectly processes GATK Mutect2 vcf INFO field AS_SB_TABLE
vcf
AS_SB_TABLE
readVcf
Mutect2
VariantAnnotation
14 months ago
therealgenna
• 0
0
votes
3
replies
1.0k
views
Add GP values to VCF
VariantAnnotation
16 months ago • updated 15 months ago
Stephanie M. Gogarten
▴ 870
0
votes
1
reply
1.5k
views
Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123
VariantFiltering
Alignment
VariantAnnotation
updated 18 months ago by
James W. MacDonald
65k • written 18 months ago by
Mohamed
▴ 30
2
votes
4
replies
945
views
Error message from protein coding prediction with VariantAnnotation
R
VariantAnnotation
19 months ago
rwan.work
• 0
0
votes
2
replies
749
views
Error message from protein coding prediction with VariantAnnotation
R
VariantAnnotation
19 months ago
rwan.work
• 0
0
votes
2
replies
3.9k
views
VariantAnnotation R Package - Merging Two VCF files
VariantAnnotation
VariantAnnotation
VariantAnnotation
VariantAnnotation
written 10.2 years ago by
Fong Chun Chan
▴ 320
0
votes
2
replies
2.6k
views
merging VCF files
VariantAnnotation
VariantAnnotation
VariantAnnotation
VariantAnnotation
written 11.3 years ago by
Stephanie M. Gogarten
▴ 870
1
vote
4
replies
5.6k
views
merging VCF files
VariantAnnotation
VariantAnnotation
VariantAnnotation
VariantAnnotation
written 11.2 years ago by
Valerie Obenchain
★ 6.8k
0
votes
3
replies
1.0k
views
Problem with intronic variants in VariantAnnotation
VariantAnnotation
updated 2.2 years ago by
Raül
• 0 • written 2.3 years ago by
paolo.provero
• 0
0
votes
2
replies
1.0k
views
Reading vcf file with readVcf
VariantAnnotation
2.6 years ago
aurelien.dejode
• 0
0
votes
2
replies
812
views
Multiple exons for predictCoding() from VariantAnnotation (use phase information from gff3 file)?
VariantAnnotation
updated 2.7 years ago by
Hervé Pagès
16k • written 2.8 years ago by
Kasper_holm2
• 0
0
votes
1
reply
883
views
GRanges object out-of-bound
VariantAnnotation
updated 2.7 years ago by
Vincent J. Carey, Jr.
6.7k • written 2.8 years ago by
Kasper_holm2
• 0
0
votes
5
replies
1.3k
views
installation error: Error in setIs(class2, cli, extensionObject = obji, doComplete = FALSE and setClass() for chromVAR and VariantAnnotation
Install
VariantAnnotation
Bioconductor
chromVAR
updated 2.7 years ago by
Vincent J. Carey, Jr.
6.7k • written 2.7 years ago by
Hannah
• 0
0
votes
0
replies
601
views
Annotate mutations on DNA level to splice transcripts
VariantAnnotation
2.8 years ago
Kasper_holm2
• 0
0
votes
4
replies
1.6k
views
Error of read in large vcf file using readVcf
SomaticSignatures
VariantAnnotation
updated 2.8 years ago by
James W. MacDonald
65k • written 2.8 years ago by
xiw588
• 0
0
votes
2
replies
1.2k
views
VariantAnnotation::readVcf not reading variants
VariantAnnotation
updated 3.0 years ago by
James W. MacDonald
65k • written 3.0 years ago by
peiwen.li
• 0
1
vote
12
replies
3.0k
views
readVcf does not recognize tabix index
VariantAnnotation
readvcf
tabix
updated 3.1 years ago by
Vincent J. Carey, Jr.
6.7k • written 3.1 years ago by
naive
• 0
0
votes
2
replies
2.2k
views
VCF File too large for tabix. Best option to make it usable with R?
samtools
tabix
VariantAnnotation
VCFArray
updated 3.1 years ago by
Vincent J. Carey, Jr.
6.7k • written 3.2 years ago by
naive
• 0
0
votes
2
replies
1.3k
views
readVCF requires the argument "genome". What does it stand for?
Genome
readVcf
VariantAnnotation
3.1 years ago
naive
• 0
2
votes
2
replies
1.3k
views
Obtaining Comments From VCF Header
VariantAnnotation
VCFHeader
updated 3.8 years ago by
Martin Morgan
25k • written 3.8 years ago by
Dario Strbenac
★ 1.5k
3
votes
2
replies
1.3k
views
Import or Subset VCF PASS Variants
VariantAnnotation
subset
ScanVcfParam
updated 4.0 years ago by
Martin Morgan
25k • written 4.0 years ago by
Dario Strbenac
★ 1.5k
0
votes
2
replies
1.1k
views
Extract structural variant and flanking sequence from VCF and fasta, in R
VariantAnnotation
Bioconductor
VCF
Structural variants
R
updated 4.1 years ago by
Martin Morgan
25k • written 4.1 years ago by
W. van Rengs
• 0
0
votes
1
reply
658
views
Can strand be set to minus in VRanges objects?
VariantAnnotation
updated 4.3 years ago by
James W. MacDonald
65k • written 4.3 years ago by
david.mas
• 0
0
votes
1
reply
1.2k
views
FilterVCF Filter '' failed: shape of 'skeleton' is not compatible with 'NROW(flesh)'
variantAnnotation
updated 4.6 years ago by
Martin Morgan
25k • written 4.6 years ago by
b.curran
• 0
2
votes
3
replies
1.5k
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 4.8 years ago by
Steve Lianoglou
★ 13k • written 4.8 years ago by
james.dalgleish
▴ 30
2
votes
3
replies
946
views
VariantAnnotation - subset multi-allele variants
variantAnnotation
updated 4.8 years ago by
Michael Lawrence
★ 11k • written 4.8 years ago by
user1986
• 0
0
votes
1
reply
771
views
negative AD value interfering with readVcfasVRanges
VariantAnnotation
updated 4.9 years ago by
Michael Lawrence
★ 11k • written 4.9 years ago by
TRASA
• 0
0
votes
3
replies
1.0k
views
rbind VCF Two Objects Column Names Error
VariantAnnotation
VCF
4.9 years ago
Dario Strbenac
★ 1.5k
0
votes
0
replies
773
views
predictCoding warning message: serious or not?
software error
annotation
VariantAnnotation
updated 5.1 years ago by
shepherl
3.9k • written 5.1 years ago by
longsong
• 0
2
votes
3
replies
1.4k
views
Error in VCF parsing with VariantAnnotation
software error
VariantAnnotation
ensemblVEP
updated 5.1 years ago by
Valerie Obenchain
★ 6.8k • written 5.1 years ago by
mumichae
▴ 20
3
votes
8
replies
3.1k
views
Create protein sequences including variants from a VCF file
VariantAnnotation
customProDB
5.2 years ago • updated 5.1 years ago
daniel.magnus.bader
▴ 40
0
votes
1
reply
940
views
VariantAnnotation fails to load VCF record
variantannotation
5.4 years ago
Daniel Cameron
▴ 40
0
votes
6
replies
1.5k
views
How to prepare .vcf for seqCAT
seqCAT
variantannotation
gatk
updated 5.4 years ago by
erikfas
▴ 30 • written 5.4 years ago by
abe
• 0
0
votes
1
reply
835
views
writeVcf save invalid vcf with metadata out of order
variantannotation
updated 5.5 years ago by
Valerie Obenchain
★ 6.8k • written 5.5 years ago by
alessandro.pastore
▴ 20
1
vote
7
replies
3.1k
views
Data from ##SAMPLE lines in VCF?
variantannotation
coldata
updated 5.6 years ago by
Valerie Obenchain
★ 6.8k • written 5.6 years ago by
lvclark
▴ 10
3
votes
3
replies
1.3k
views
Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
variantannotation
updated 5.8 years ago by
Valerie Obenchain
★ 6.8k • written 5.8 years ago by
goldberg.jm
▴ 10
3
votes
4
replies
1.7k
views
Problem when transforming Platypus vcf to VRanges
variantannotation
vcf
readvcf
vranges
updated 5.8 years ago by
Michael Lawrence
★ 11k • written 5.8 years ago by
david.mas
• 0
0
votes
2
replies
1.2k
views
Error: invalid class "VRanges" object
variantannotation
VRanges
R
Rle
updated 5.9 years ago by
Valerie Obenchain
★ 6.8k • written 5.9 years ago by
Jayendra Shinde
• 0
0
votes
2
replies
1.2k
views
VariantAnnotation::locateVariants error coming from XVector
variantannotation
xvector
iranges
5.9 years ago
Vivek.b
▴ 100
0
votes
2
replies
1.6k
views
filtering a VCF file based on genotype
variantannotation
updated 6.0 years ago by
Valerie Obenchain
★ 6.8k • written 6.0 years ago by
Bogdan
▴ 670
0
votes
1
reply
1.2k
views
VariantAnnotation and filtering a VCF
variantannotation
6.0 years ago
Bogdan
▴ 670
50 results • Page
1 of 1
Recent ...
Replies
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
Awards
• All
Popular Question
to
Gordon Smyth
50k
Popular Question
to
Zainab
• 0
Popular Question
to
Theo
▴ 10
Popular Question
to
gene_bioconductor
▴ 10
Popular Question
to
rohitsatyam102
▴ 20
Locations
• All
France,
2 minutes ago
The city by the bay,
26 minutes ago
WEHI, Melbourne, Australia,
37 minutes ago
Iran,
1 hour ago
San Diego,
2 hours ago
Traffic: 535 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