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News:
Ensembl 103 has been released
biomaRt
ensembldb
Ensembl
ensemblVEP
Biomart
15 days ago
mchakiachvili
• 0
• updated 15 days ago
dobby.goes.science
• 0
0
votes
2
replies
224
views
questions when installing 'Ensembl VEP' and R package 'ensemblVEP'
R
ensemblVEP
gene annotation
Variant Effect Predictor
Ensembl VEP
19 months ago
ycchang
• 0
2
votes
3
replies
305
views
Error in VCF parsing with VariantAnnotation
software error
VariantAnnotation
ensemblVEP
24 months ago
mumichae
• 20
• updated 23 months ago
Valerie Obenchain
♦ 6.7k
2
votes
5
replies
547
views
ensemblVEP: "Ensembl VEP is not installed in your path."
software error
ensemblVEP
24 months ago
patrick.turko
• 10
• updated 24 months ago
Martin Morgan
25k
0
votes
4
replies
417
views
ensemblVEP supported versions, and troubleshooting
ensemblVEP
3.0 years ago
Janet Young
• 740
• updated 3.0 years ago
shepherl
2.5k
0
votes
0
replies
535
views
error using ensemblVEP v88 when querying rs67418256 with basic(param_vep)$everything=TRUE
ensemblvep
3.8 years ago
mlrubio
• 0
0
votes
0
replies
839
views
problem using ensemblVEP with GRC37
ensemblvep
grch37
3.8 years ago
mikko.arvas
• 0
0
votes
1
reply
412
views
ensemblVEP problem with MySQL database
ensemblvep
4.6 years ago
clairelsimpson
• 10
2
votes
4
replies
610
views
parseCSQToGRanges() : mcols are all factors, despite some numeric fields
ensemblVEP
4.8 years ago
kevin.rue
• 300
• updated 4.8 years ago
Martin Morgan
25k
2
votes
3
replies
1.4k
views
ensemblVEP support for Ensembl API version 78
ensemblvep
6.2 years ago
Moiz Bootwalla
• 50
• updated 6.2 years ago
Valerie Obenchain
♦ 6.7k
0
votes
2
replies
1.3k
views
ensemblVEP, variant_effect_predictor versions and release schedule
Transcription
HapMap
PolyPhen
SIFT
convert
genomes
ensemblVEP
Transcription
HapMap
SIFT
7.2 years ago
Thomas Sandmann
• 30
• updated 7.1 years ago
Valerie Obenchain
♦ 6.7k
0
votes
0
replies
688
views
ensemblVEP, variant_effect_predictor versions and release schedule
Cancer
MLInterfaces
bridge
ensemblVEP
AnnotationHub
Cancer
MLInterfaces
bridge
ensemblVEP
7.2 years ago
Valerie Obenchain
♦ 6.7k
0
votes
0
replies
628
views
zero-row result breaks select() on PolyPhen.Hsapiens.* and SIFT.Hsapiens.*
VariantAnnotation
Annotation
PolyPhen
SIFT
annotate
VariantAnnotation
ensemblVEP
Annotation
7.3 years ago
Valerie Obenchain
♦ 6.7k
0
votes
5
replies
768
views
ensemblVEP, variant_effect_predictor versions and release schedule
ensemblVEP
ensemblVEP
7.4 years ago
Guest User
♦ 12k
• updated 7.4 years ago
Valerie Obenchain
♦ 6.7k
0
votes
5
replies
1.1k
views
ensemblVEP: passing on coverage / frequency information
Coverage
VariantTools
ensemblVEP
Coverage
VariantTools
ensemblVEP
7.9 years ago
Guest User
♦ 12k
• updated 7.9 years ago
Valerie Obenchain
♦ 6.7k
15 results • Page
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Recent ...
Replies
Comment: Removing rows (countData) from a DESeq Object
by
Bine
• 0
Thank you I will check this documentation!
Comment: Removing rows (countData) from a DESeq Object
by
ATpoint
• 470
> View(dds0) doesnt work Yes, that is expected. The DESeqDataSet is a container, not a specific assay itself so you first have to access t…
Comment: Removing rows (countData) from a DESeq Object
by
Bine
• 0
Thank you very much. Sry for not explaining it clearly enough. It is great that the colData will be filtered automatically. What I want to…
Comment: Removing rows (countData) from a DESeq Object
by
ATpoint
• 470
The DESeqDataSet is basically a SummarizedExperiment, so standard subsetting operations apply. The crux of SE is that you do not have to ma…
Comment: DiffBind dba.report() output: Is "concentration" normalized?
by
amwa
• 0
Sorry to dredge up this post years later, but does this mean that there is no other modification to the raw read counts aside from the log2…
Votes
Comment: Removing rows (countData) from a DESeq Object
Comment: Removing rows (countData) from a DESeq Object
Answer: Using group instead of interaction term on a custom edited matrix
Comment: Best way to handle tags of bam files
Answer: Using group instead of interaction term on a custom edited matrix
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