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ensemblvep
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0
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397
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RFC: significant changes to ensemblVEP package
VariantAnnotation
ensemblVEP
15 months ago
Vincent J. Carey, Jr.
6.7k
0
votes
1
reply
623
views
Differential express genes in one group across all time points
DESeq2
edgeR
BP4RNAseq
ensemblVEP
updated 24 months ago by
Michael Love
43k • written 24 months ago by
DHARMESH
• 0
2
votes
3
replies
2.4k
views
How to use a specific Bioconductor version in custom Dockerfile
singularity
ensemblVEP
docker
2.3 years ago
jtaylor-predicine
• 0
0
votes
1
reply
1.0k
views
Ensembl REST API Endpoints
ensemblVEP
EnsDb.Hsapiens.v79
updated 3.3 years ago by
Kevin Blighe
★ 4.0k • written 3.3 years ago by
anasjamshed1994
• 0
0
votes
2
replies
1.7k
views
News:
Ensembl 103 has been released
biomaRt
ensembldb
Ensembl
ensemblVEP
Biomart
4.1 years ago • updated 3.9 years ago
mchakiachvili
▴ 20
0
votes
2
replies
1.5k
views
questions when installing 'Ensembl VEP' and R package 'ensemblVEP'
R
ensemblVEP
gene annotation
Variant Effect Predictor
Ensembl VEP
5.7 years ago
ycchang
• 0
2
votes
3
replies
1.9k
views
Error in VCF parsing with VariantAnnotation
software error
VariantAnnotation
ensemblVEP
updated 6.1 years ago by
Valerie Obenchain
★ 6.8k • written 6.1 years ago by
mumichae
▴ 20
2
votes
5
replies
2.7k
views
ensemblVEP: "Ensembl VEP is not installed in your path."
software error
ensemblVEP
updated 6.1 years ago by
Martin Morgan
25k • written 6.1 years ago by
patrick.turko
▴ 10
0
votes
4
replies
1.7k
views
ensemblVEP supported versions, and troubleshooting
ensemblVEP
updated 7.1 years ago by
shepherl
4.1k • written 7.1 years ago by
Janet Young
▴ 740
0
votes
0
replies
1.3k
views
error using ensemblVEP v88 when querying rs67418256 with basic(param_vep)$everything=TRUE
ensemblvep
7.9 years ago
mlrubio
• 0
0
votes
0
replies
1.9k
views
problem using ensemblVEP with GRC37
ensemblvep
grch37
7.9 years ago
mikko.arvas
• 0
0
votes
1
reply
1.1k
views
ensemblVEP problem with MySQL database
ensemblvep
8.7 years ago
clairelsimpson
▴ 10
2
votes
4
replies
1.7k
views
parseCSQToGRanges() : mcols are all factors, despite some numeric fields
ensemblVEP
updated 8.9 years ago by
Martin Morgan
25k • written 8.9 years ago by
kevin.rue
▴ 350
2
votes
3
replies
2.3k
views
ensemblVEP support for Ensembl API version 78
ensemblvep
updated 10.3 years ago by
Valerie Obenchain
★ 6.8k • written 10.3 years ago by
Moiz Bootwalla
▴ 50
0
votes
2
replies
2.5k
views
ensemblVEP, variant_effect_predictor versions and release schedule
Transcription
HapMap
PolyPhen
SIFT
convert
genomes
ensemblVEP
Transcription
HapMap
SIFT
updated 11.2 years ago by
Valerie Obenchain
★ 6.8k • written 11.3 years ago by
Thomas Sandmann
▴ 30
0
votes
0
replies
1.3k
views
ensemblVEP, variant_effect_predictor versions and release schedule
Cancer
MLInterfaces
bridge
ensemblVEP
AnnotationHub
Cancer
MLInterfaces
bridge
ensemblVEP
11.3 years ago
Valerie Obenchain
★ 6.8k
0
votes
0
replies
1.5k
views
zero-row result breaks select() on PolyPhen.Hsapiens.* and SIFT.Hsapiens.*
VariantAnnotation
Annotation
PolyPhen
SIFT
annotate
VariantAnnotation
ensemblVEP
Annotation
11.4 years ago
Valerie Obenchain
★ 6.8k
0
votes
5
replies
1.5k
views
ensemblVEP, variant_effect_predictor versions and release schedule
ensemblVEP
ensemblVEP
updated 11.5 years ago by
Valerie Obenchain
★ 6.8k • written 11.5 years ago by
Guest User
★ 13k
0
votes
5
replies
2.4k
views
ensemblVEP: passing on coverage / frequency information
Coverage
VariantTools
ensemblVEP
Coverage
VariantTools
ensemblVEP
updated 12.0 years ago by
Valerie Obenchain
★ 6.8k • written 12.0 years ago by
Guest User
★ 13k
19 results • Page
1 of 1
Recent ...
Replies
Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
by
Luca
• 0
Sorry for reviving this 1 month later, but I was reading about size factor estimation, and just wanted to add my findings if anyone stumble…
Comment: DiffBind can't find a DAR
by
ATpoint
★ 4.8k
"My cake does not look as advertised in the recipe", with this sloppy sentence I hope you understand that you need to give people details, …
Comment: DESeq - help with pair wise comparisons
by
bd2000
▴ 30
Follow up question, is this the correct way to extract results? ```r results <- results(ddsObj, list(c("GroupControl.Followup", "GroupTrea…
Comment: DESeq: Gene is not flagged as differentially expressed despite count data showin
by
ktz
• 0
Thank you for your reply! I would love to know your thoughts on the plots I've included above. > 'Are the differences between groups lar…
Comment: DESeq: Gene is not flagged as differentially expressed despite count data showin
by
ktz
• 0
I also realised that the other gene I pointed out that was flagged as DE but had similar count differences also shows that rep1 is lower th…
Votes
Comment: DESeq - help with pair wise comparisons
Answer: Is random access by row index possible for an indexed VCF file?
Answer: Is random access by row index possible for an indexed VCF file?
Answer: SingleR with multiple single cell references
Answer: SingleR with multiple single cell references
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68k
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