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VariantAnnotation
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reset
0
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0
replies
1.3k
views
Subsetting vcf file by subject
VariantAnnotation
Annotation
cycle
VariantAnnotation
VariantAnnotation
Annotation
cycle
12.6 years ago
Valerie Obenchain
★ 6.8k
0
votes
0
replies
1.2k
views
Error when try VariantAnnotation filterVcf vignette example
VariantAnnotation
VariantAnnotation
VariantAnnotation
VariantAnnotation
12.6 years ago
Paul Shannon
▴ 750
0
votes
1
reply
2.3k
views
Help needed! What wrong with VariantAnnotation and TCGA vcfs
VariantAnnotation
genomes
VariantAnnotation
VariantAnnotation
genomes
VariantAnnotation
updated 12.6 years ago by
Martin Morgan
25k • written 12.6 years ago by
ying chen
▴ 340
0
votes
3
replies
2.3k
views
trouble installing affycoretools for R 3.0
VariantAnnotation
GO
BSgenome
affycoretools
BSgenome
VariantAnnotation
ggbio
GO
BSgenome
updated 12.7 years ago by
James W. MacDonald
68k • written 12.7 years ago by
Jenny Drnevich
★ 2.0k
0
votes
1
reply
976
views
Subsetting vcf file by subject
VariantAnnotation
Annotation
VariantAnnotation
VariantAnnotation
Annotation
VariantAnnotation
updated 12.7 years ago by
Valerie Obenchain
★ 6.8k • written 12.7 years ago by
Taub, Margaret
▴ 10
1
vote
4
replies
6.4k
views
merging VCF files
VariantAnnotation
VariantAnnotation
VariantAnnotation
VariantAnnotation
written 12.8 years ago by
Valerie Obenchain
★ 6.8k
1
vote
3
replies
1.7k
views
VariantAnnotation package with snp location
SNP
VariantAnnotation
VariantAnnotation
SNP
VariantAnnotation
VariantAnnotation
updated 12.8 years ago by
Tim Triche
★ 4.2k • written 12.8 years ago by
Fabrice Tourre
▴ 970
0
votes
3
replies
1.3k
views
VariantAnnotation: fine define Locating variants in and around genes
SNP
VariantAnnotation
VariantAnnotation
SNP
VariantAnnotation
VariantAnnotation
updated 12.8 years ago by
Valerie Obenchain
★ 6.8k • written 12.8 years ago by
Fabrice Tourre
▴ 970
0
votes
2
replies
1.8k
views
geneid to gene name conversion
VariantAnnotation
convert
biomaRt
VariantAnnotation
VariantAnnotation
convert
biomaRt
updated 12.9 years ago by
Paul Shannon
▴ 750 • written 12.9 years ago by
Matthew Liebers
▴ 10
0
votes
2
replies
1.7k
views
VariantAnnotation ALT Field
VariantAnnotation
VariantAnnotation
VariantAnnotation
VariantAnnotation
updated 13.0 years ago by
Paul Shannon
▴ 750 • written 13.0 years ago by
Samuel Younkin
▴ 60
0
votes
6
replies
1.9k
views
Why is writeVcf() slow?
VariantAnnotation
VariantAnnotation
VariantAnnotation
VariantAnnotation
updated 13.1 years ago by
Valerie Obenchain
★ 6.8k • written 13.1 years ago by
Peter Hickey
▴ 760
0
votes
1
reply
1.7k
views
Subsetting "sites only" VCF objects
VariantAnnotation
VariantAnnotation
VariantAnnotation
VariantAnnotation
updated 13.3 years ago by
Valerie Obenchain
★ 6.8k • written 13.3 years ago by
Richard Pearson
▴ 80
0
votes
17
replies
3.5k
views
problems with strand in predictCoding
VariantAnnotation
Annotation
BSgenome
BSgenome
VariantAnnotation
VariantAnnotation
BSgenome
updated 13.6 years ago by
bnorthoff@web.de
▴ 20 • written 13.6 years ago by
Jeremiah Degenhardt
▴ 50
0
votes
3
replies
1.7k
views
Complementing alleles in a VCF
VariantAnnotation
BSgenome
BSgenome
genomes
VariantAnnotation
VariantAnnotation
BSgenome
updated 13.6 years ago by
Martin Morgan
25k • written 13.6 years ago by
Alex Gutteridge
▴ 650
0
votes
4
replies
1.9k
views
Finding coding SNPs with predictCoding
SNP
VariantAnnotation
BSgenome
SNPlocs
BSgenome
VariantAnnotation
SNP
VariantAnnotation
updated 13.8 years ago by
Valerie Obenchain
★ 6.8k • written 13.8 years ago by
Alex Gutteridge
▴ 650
0
votes
0
replies
1.2k
views
Bioconductor Digest, Vol 106, Issue 21
SNP
Microarray
VariantAnnotation
Annotation
cdf
probe
affy
limma
PROcess
oligo
xps
SNP
14.0 years ago
Jing Huang
▴ 380
0
votes
0
replies
1.2k
views
rsamtools scanBcf segfault
VariantAnnotation
Rsamtools
VariantAnnotation
VariantAnnotation
Rsamtools
VariantAnnotation
14.2 years ago
Valerie Obenchain
★ 6.8k
217 results • Page
5 of 5
Recent ...
Replies
Comment: Question about DESeq2 Design for Paired Treatment Study
by
ATpoint
★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR
by
efoss
▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma
by
Gordon Smyth
53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
by
Ahmed Salah
• 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR
by
JKim
• 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Votes
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
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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