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
1
vote
4
replies
5.6k
views
merging VCF files
VariantAnnotation
VariantAnnotation
VariantAnnotation
VariantAnnotation
written 11.2 years ago by
Valerie Obenchain
★ 6.8k
1
vote
2
replies
4.8k
views
ICU init failed: U_FILE_ACCESS_ERROR while loading library "VariantAnnotation"
variantannotation
library
error
updated 8.7 years ago by
Valerie Obenchain
★ 6.8k • written 8.7 years ago by
kmu004
▴ 50
3
votes
2
replies
4.8k
views
Add data to Vcf Info Field
variantannotation
updated 9.5 years ago by
Valerie Obenchain
★ 6.8k • written 9.5 years ago by
Moiz Bootwalla
▴ 50
0
votes
4
replies
4.7k
views
Question: How can I filter a vcf file by DP and GQ using the R package VariantAnnotation?
VariantAnnotation
Sample Read Depth
Phred-Scaled Genotype Quality
vcf
updated 9.1 years ago by
Valerie Obenchain
★ 6.8k • written 9.1 years ago by
r.jaffe
• 0
0
votes
21
replies
4.3k
views
VariantAnnotation Errors and void outputs
variantannotation
readvcf
9.0 years ago
pifferdavide
• 0
1
vote
5
replies
4.3k
views
Converting a DNAStringSetList to characters quickly
readVcf
DNAStringSet
DNAStringSetList
variantannotation
readvcf
9.0 years ago
dan.gatti
• 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
1
reply
3.7k
views
Subset VCF files using multiple criteria
vcf
variantannotation
granges
8.2 years ago
georgewwp
• 0
3
votes
4
replies
3.6k
views
Quality filtering of exactSNP-generated VCF files
exactSNP
qc
variantannotation
updated 9.5 years ago by
Wei Shi
★ 3.6k • written 9.5 years ago by
daniel.silvestre
▴ 100
0
votes
1
reply
3.4k
views
Multi-sample VCF file and filterVcf
VariantAnnotation
Annotation
VariantAnnotation
VariantAnnotation
Annotation
VariantAnnotation
updated 10.0 years ago by
Valerie Obenchain
★ 6.8k • written 10.0 years ago by
Guest User
★ 13k
2
votes
6
replies
3.3k
views
Import of vcf with VariantAnnotation
variantannotation
somaticsignatures
9.5 years ago
Anna N.
• 0
5
votes
6
replies
3.2k
views
Error in reading 1000 genomes data
variantannotation
updated 8.2 years ago by
Martin Morgan
25k • written 9.5 years ago by
Wade Copeland
▴ 20
3
votes
9
replies
3.1k
views
Annotate VCFs with Cosmic (ExAC etc.) fields
variantannotation
cosmic
exac
updated 7.5 years ago by
Martin Morgan
25k • written 7.5 years ago by
markus.riester
▴ 130
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
8
replies
3.1k
views
Create protein sequences including variants from a VCF file
VariantAnnotation
customProDB
5.2 years ago
daniel.magnus.bader
▴ 40
3
votes
5
replies
3.0k
views
Add Custom Annotations to Multi-Sample VCF with VariantAnnotation() package
variantannotation
granges
DNAStringSetList
findoverlaps
Vranges
9.2 years ago
summerela
• 0
0
votes
2
replies
3.0k
views
Problem reading VCF file using readVcf from package VariantAnnotation
VariantAnnotation
VariantAnnotation
VariantAnnotation
VariantAnnotation
updated 11.0 years ago by
Valerie Obenchain
★ 6.8k • written 11.0 years ago by
UBod
▴ 290
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
4
votes
10
replies
2.9k
views
Best way to import from multiple VCF files?
variantannotation
updated 7.8 years ago by
shepherl
3.9k • written 7.8 years ago by
Kipper Fletez-Brant
▴ 150
0
votes
10
replies
2.8k
views
Incorrect row names when a VCF has multiple ALTs.
variantannotation
vcf
updated 9.5 years ago by
Valerie Obenchain
★ 6.8k • written 9.5 years ago by
bicycle1885
• 0
1
vote
12
replies
2.8k
views
VariantAnnotation: no method for function 'path' for signature 'character'
variantannotation
readvcf
readgt
updated 9.4 years ago by
Valerie Obenchain
★ 6.8k • written 9.4 years ago by
Kipper Fletez-Brant
▴ 150
0
votes
2
replies
2.8k
views
Problem using biocLite() to update packages
biocLite
BiocInstaller
variantannotation
updated 6.5 years ago by
James W. MacDonald
65k • written 6.5 years ago by
Jenny Drnevich
★ 2.0k
0
votes
7
replies
2.8k
views
VariantAnnotation: Performance and memory issues in readVcf
VariantAnnotation
PROcess
Rsamtools
VariantAnnotation
VariantAnnotation
PROcess
Rsamtools
updated 11.0 years ago by
Vincent J. Carey, Jr.
6.7k • written 11.0 years ago by
UBod
▴ 290
0
votes
7
replies
2.8k
views
append to bgzipped VCF file
variantannotation
tabix
updated 8.5 years ago by
Michael Lawrence
★ 11k • written 8.5 years ago by
TimothéeFlutre
▴ 80
0
votes
8
replies
2.8k
views
Best practices to find intersection among variants
VariantAnnotation
genomes
VariantAnnotation
VariantAnnotation
genomes
VariantAnnotation
updated 9.7 years ago by
Julian Gehring
★ 1.3k • written 9.7 years ago by
Marco Blanchette
▴ 220
2
votes
9
replies
2.7k
views
ReadVCF not reading samples
readvcf
vcf
variantannotation
9.0 years ago
askates
▴ 10
0
votes
6
replies
2.7k
views
readVcf shape of 'skeleton' is not compatible with 'NROW(flesh)'
variantannotation
updated 8.9 years ago by
Valerie Obenchain
★ 6.8k • written 8.9 years ago by
Miss Agnieszka Aleksandra Golicz
▴ 40
0
votes
17
replies
2.6k
views
problems with strand in predictCoding
VariantAnnotation
Annotation
BSgenome
BSgenome
VariantAnnotation
VariantAnnotation
BSgenome
updated 12.0 years ago by
bnorthoff@web.de
▴ 20 • written 12.0 years ago by
Jeremiah Degenhardt
▴ 50
2
votes
5
replies
2.6k
views
VariantAnnotation: Error with ScanVcfParam
variantannotation
vcf
readvcf
filtervcf
scanvcfparam
6.8 years ago
Didi
▴ 10
0
votes
2
replies
2.6k
views
merging VCF files
VariantAnnotation
VariantAnnotation
VariantAnnotation
VariantAnnotation
written 11.3 years ago by
Stephanie M. Gogarten
▴ 870
2
votes
6
replies
2.6k
views
extracting Allele Read Counts - part2
rsamtools
variantannotation
updated 7.1 years ago by
James W. MacDonald
65k • written 7.1 years ago by
Bogdan
▴ 670
0
votes
23
replies
2.6k
views
VariantAnnotation geno function
variantannotation
7.5 years ago
ribioinfo
▴ 100
2
votes
5
replies
2.5k
views
Plot data from VCF using Gviz?
gviz
variantannotation
vcf
updated 8.5 years ago by
Valerie Obenchain
★ 6.8k • written 8.5 years ago by
Johannes Rainer
★ 2.0k
0
votes
1
reply
2.5k
views
help with analysis of genotyping data from Illumina HumanOmni5-4v1_B chip
SNP
VariantAnnotation
Annotation
probe
VariantAnnotation
GWASTools
SNP
VariantAnnotation
updated 9.9 years ago by
Stephanie M. Gogarten
▴ 870 • written 9.9 years ago by
Abhishek Pratap
▴ 160
2
votes
2
replies
2.4k
views
Vranges (somatic signature) VariantAnnotation
software error
variantannotation
updated 9.6 years ago by
Steve Lianoglou
★ 13k • written 9.6 years ago by
humaasif79
• 0
1
vote
23
replies
2.4k
views
Distance calculation for variants in intergenic regions
locatevariants
variantannotation
genomicfeatures
updated 7.5 years ago by
Michael Lawrence
★ 11k • written 7.5 years ago by
Lna
• 0
0
votes
20
replies
2.3k
views
VariantAnnotation function getTranscriptSeqs() gives error "object '.makeUCSCTxListFromGRangesList' not found"
variantannotation
8.7 years ago • updated 8.5 years ago
Tjeerd Dijkstra
• 0
1
vote
10
replies
2.3k
views
predictCoding error DNAStringSet_translate
variantannotation
predict coding
updated 9.1 years ago by
Valerie Obenchain
★ 6.8k • written 9.1 years ago by
Miss Agnieszka Aleksandra Golicz
▴ 40
3
votes
3
replies
2.3k
views
VariantAnnotation Installation Failure
VariantAnnotation
updated 6.9 years ago by
Valerie Obenchain
★ 6.8k • written 6.9 years ago by
andrew.j.skelton73
▴ 370
0
votes
2
replies
2.3k
views
VariantAnnotation Installation Error RSQLite
VariantAnnotation
RSQLite
9.4 years ago
remi.tournebize
▴ 10
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
2
votes
3
replies
2.2k
views
Metadata Missing from vcf when reading in with readVcfAsVRanges
variantannotation
vranges
readvcf
readvcfasvranges
metadata
9.2 years ago
summerela
• 0
0
votes
6
replies
2.2k
views
Error using readVcf
gwastools
variantannotation
updated 6.9 years ago by
Stephanie M. Gogarten
▴ 870 • written 6.9 years ago by
Lna
• 0
1
vote
4
replies
2.2k
views
variantAnnotation::locateVariants() with AllVariants(): why do some input variants not get annotated?
variantannotation
locatevariants
8.7 years ago
Jakob Goldmann
• 0
0
votes
3
replies
2.2k
views
vcf postion extract
vcf
variantannotation
position
updated 8.3 years ago by
Martin Morgan
25k • written 8.3 years ago by
1000G_Q
• 0
7
votes
4
replies
2.1k
views
BiocGenerics built with R 3.4.2 changes behaviour
biocgenerics
iranges
variantannotation
updated 6.6 years ago by
Hervé Pagès
16k • written 6.6 years ago by
ginggs
▴ 40
0
votes
5
replies
2.1k
views
Error installing VariantAnnotation with bioconductor/devel_core
install
variantannotation
9.2 years ago
kforner
• 0
1
vote
3
replies
2.1k
views
annotation of SV (Structural Variants)
variantannotation
annotationhub
7.1 years ago
Bogdan
▴ 670
4
votes
4
replies
2.0k
views
readVcfAsVRanges + FilterRules
variantannotation
filterVcf
readvcfasvranges
filterRules
updated 9.2 years ago by
Martin Morgan
25k • written 9.2 years ago by
Sigve Nakken
▴ 50
0
votes
4
replies
2.0k
views
'namespace:Biostrings' error when installing VariantAnnotation
VariantAnnotation
VariantAnnotation
VariantAnnotation
VariantAnnotation
updated 10.9 years ago by
Steve Lianoglou
★ 13k • written 10.9 years ago by
Thomas Damm Als
▴ 20
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
Taiwan,
just now
Ireland,
27 minutes ago
United States,
31 minutes ago
France,
41 minutes ago
WEHI, Melbourne, Australia,
1 hour ago
Traffic: 537 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