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ensemblvep
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RFC: significant changes to ensemblVEP package
VariantAnnotation
ensemblVEP
3 months ago
Vincent J. Carey, Jr.
6.7k
0
votes
1
reply
416
views
Differential express genes in one group across all time points
DESeq2
edgeR
BP4RNAseq
ensemblVEP
updated 12 months ago by
Michael Love
41k • written 12 months ago by
DHARMESH
• 0
2
votes
3
replies
1.5k
views
How to use a specific Bioconductor version in custom Dockerfile
singularity
ensemblVEP
docker
17 months ago
jtaylor-predicine
• 0
0
votes
1
reply
786
views
Ensembl REST API Endpoints
ensemblVEP
EnsDb.Hsapiens.v79
updated 2.3 years ago by
Kevin Blighe
★ 3.9k • written 2.3 years ago by
anasjamshed1994
• 0
0
votes
2
replies
1.3k
views
News:
Ensembl 103 has been released
biomaRt
ensembldb
Ensembl
ensemblVEP
Biomart
3.2 years ago • updated 3.0 years ago
mchakiachvili
▴ 20
0
votes
2
replies
1.1k
views
questions when installing 'Ensembl VEP' and R package 'ensemblVEP'
R
ensemblVEP
gene annotation
Variant Effect Predictor
Ensembl VEP
4.8 years ago
ycchang
• 0
2
votes
3
replies
1.4k
views
Error in VCF parsing with VariantAnnotation
software error
VariantAnnotation
ensemblVEP
updated 5.1 years ago by
Valerie Obenchain
★ 6.8k • written 5.1 years ago by
mumichae
▴ 20
2
votes
5
replies
2.2k
views
ensemblVEP: "Ensembl VEP is not installed in your path."
software error
ensemblVEP
updated 5.2 years ago by
Martin Morgan
25k • written 5.2 years ago by
patrick.turko
▴ 10
0
votes
4
replies
1.2k
views
ensemblVEP supported versions, and troubleshooting
ensemblVEP
updated 6.1 years ago by
shepherl
3.9k • written 6.1 years ago by
Janet Young
▴ 740
0
votes
0
replies
1.1k
views
error using ensemblVEP v88 when querying rs67418256 with basic(param_vep)$everything=TRUE
ensemblvep
7.0 years ago
mlrubio
• 0
0
votes
0
replies
1.7k
views
problem using ensemblVEP with GRC37
ensemblvep
grch37
7.0 years ago
mikko.arvas
• 0
0
votes
1
reply
882
views
ensemblVEP problem with MySQL database
ensemblvep
7.7 years ago
clairelsimpson
▴ 10
2
votes
4
replies
1.4k
views
parseCSQToGRanges() : mcols are all factors, despite some numeric fields
ensemblVEP
updated 8.0 years ago by
Martin Morgan
25k • written 8.0 years ago by
kevin.rue
▴ 350
2
votes
3
replies
2.1k
views
ensemblVEP support for Ensembl API version 78
ensemblvep
updated 9.4 years ago by
Valerie Obenchain
★ 6.8k • written 9.4 years ago by
Moiz Bootwalla
▴ 50
0
votes
2
replies
2.2k
views
ensemblVEP, variant_effect_predictor versions and release schedule
Transcription
HapMap
PolyPhen
SIFT
convert
genomes
ensemblVEP
Transcription
HapMap
SIFT
updated 10.3 years ago by
Valerie Obenchain
★ 6.8k • written 10.3 years ago by
Thomas Sandmann
▴ 30
0
votes
0
replies
1.1k
views
ensemblVEP, variant_effect_predictor versions and release schedule
Cancer
MLInterfaces
bridge
ensemblVEP
AnnotationHub
Cancer
MLInterfaces
bridge
ensemblVEP
10.3 years ago
Valerie Obenchain
★ 6.8k
0
votes
0
replies
1.2k
views
zero-row result breaks select() on PolyPhen.Hsapiens.* and SIFT.Hsapiens.*
VariantAnnotation
Annotation
PolyPhen
SIFT
annotate
VariantAnnotation
ensemblVEP
Annotation
10.4 years ago
Valerie Obenchain
★ 6.8k
0
votes
5
replies
1.3k
views
ensemblVEP, variant_effect_predictor versions and release schedule
ensemblVEP
ensemblVEP
updated 10.6 years ago by
Valerie Obenchain
★ 6.8k • written 10.6 years ago by
Guest User
★ 13k
0
votes
5
replies
2.0k
views
ensemblVEP: passing on coverage / frequency information
Coverage
VariantTools
ensemblVEP
Coverage
VariantTools
ensemblVEP
updated 11.1 years ago by
Valerie Obenchain
★ 6.8k • written 11.1 years ago by
Guest User
★ 13k
19 results • Page
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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
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