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
96
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
27 days ago
Stevie Pederson
• 0
0
votes
1
reply
153
views
Is random access by row index possible for an indexed VCF file?
Rsamtools
VariantAnnotation
updated 8 weeks ago by
James W. MacDonald
65k • written 8 weeks ago by
maltethodberg
▴ 180
0
votes
0
replies
168
views
RFC: significant changes to ensemblVEP package
VariantAnnotation
ensemblVEP
3 months ago
Vincent J. Carey, Jr.
6.7k
0
votes
5
replies
494
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
463
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 3.5 years ago by
Dario Strbenac
★ 1.5k
0
votes
2
replies
551
views
Docker usage with Trio Bioconductor Package
VariantAnnotation
docker
trio
updated 12 months ago by
ATpoint
★ 4.1k • written 12 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
14 months ago • updated 13 months ago
davidhillis
• 0
0
votes
0
replies
486
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
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
950
views
Error message from protein coding prediction with VariantAnnotation
R
VariantAnnotation
20 months ago
rwan.work
• 0
0
votes
2
replies
755
views
Error message from protein coding prediction with VariantAnnotation
R
VariantAnnotation
20 months ago
rwan.work
• 0
0
votes
2
replies
2.6k
views
merging VCF files
VariantAnnotation
VariantAnnotation
VariantAnnotation
VariantAnnotation
written 11.3 years ago by
Stephanie M. Gogarten
▴ 870
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
1.1k
views
Reading vcf file with readVcf
VariantAnnotation
2.6 years ago
aurelien.dejode
• 0
0
votes
2
replies
814
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
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
1
reply
887
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
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
604
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 2.9 years ago by
James W. MacDonald
65k • written 2.9 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
0
votes
2
replies
2.3k
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
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
1.3k
views
readVCF requires the argument "genome". What does it stand for?
Genome
readVcf
VariantAnnotation
3.2 years ago • updated 3.1 years ago
naive
• 0
2
votes
2
replies
1.3k
views
Obtaining Comments From VCF Header
VariantAnnotation
VCFHeader
updated 3.9 years ago by
Martin Morgan
25k • written 3.9 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
660
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
951
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
772
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
777
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 5.2 years ago by
Valerie Obenchain
★ 6.8k • written 5.2 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
daniel.magnus.bader
▴ 40
0
votes
1
reply
942
views
VariantAnnotation fails to load VCF record
variantannotation
5.4 years ago
Daniel Cameron
▴ 40
0
votes
6
replies
1.6k
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
836
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 5.9 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 5.9 years ago by
Michael Lawrence
★ 11k • written 5.9 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
6.0 years ago • updated 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
0
votes
1
reply
1.1k
views
Annotating outdated SNP identifiers
variants
variantannotation
SNPlocs.Hsapiens.dbSNP150.GRCh38
biomaRt
6.2 years ago
sandmann.t
▴ 70
2
votes
2
replies
1.4k
views
[VariantAnnotation] Preserve query metadata with locateVariants()
variantannotation
locatevariants
metadata
mcols
updated 6.4 years ago by
Valerie Obenchain
★ 6.8k • written 6.4 years ago by
enricoferrero
▴ 660
50 results • Page
1 of 1
Recent ...
Replies
Comment: Extremely small p-values using Limma for proteomic data
by
Abbey
• 0
This is the code. The only part I changed was adding the contrasts.fit as you suggested. Thanks for taking a look! ``` # Load necessary …
Comment: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
Probably. I would not expect such large fold changes. But without seeing your code, who knows?
Comment: Extremely small p-values using Limma for proteomic data
by
Abbey
• 0
Thank you James! This worked to fix the p-values. However, the plot still looks one-sided... any idea what's going on with the left side?…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
That ll be helpful. Thank you.
Comment: Log-cpm values from limma
by
Shaimaa Gamal
• 0
I have performed RUVg correction and extracted W, factors of unwanted variation. According to limma guide, > In the limma approach to RNA…
Votes
Answer: Extremely small p-values using Limma for proteomic data
Bioconductor 3.19 is Released!
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Awards
• All
Popular Question
to
neilzhao
▴ 30
Popular Question
to
ATpoint
★ 4.1k
Teacher
to
Michael Love
42k
Popular Question
to
Haibo Liu
• 0
Popular Question
to
HS
▴ 10
Locations
• All
United States,
7 minutes ago
United States,
17 minutes ago
WEHI, Melbourne, Australia,
36 minutes ago
United States,
45 minutes ago
United States,
57 minutes ago
Traffic: 532 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