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ensemblVEP
•
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0
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replies
341
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RFC: significant changes to ensemblVEP package
VariantAnnotation
ensemblVEP
10 months ago
Vincent J. Carey, Jr.
6.7k
0
votes
1
reply
543
views
Differential express genes in one group across all time points
DESeq2
edgeR
BP4RNAseq
ensemblVEP
updated 19 months ago by
Michael Love
43k • written 19 months ago by
DHARMESH
• 0
2
votes
3
replies
2.0k
views
How to use a specific Bioconductor version in custom Dockerfile
singularity
ensemblVEP
docker
23 months ago
jtaylor-predicine
• 0
0
votes
1
reply
940
views
Ensembl REST API Endpoints
ensemblVEP
EnsDb.Hsapiens.v79
updated 2.9 years ago by
Kevin Blighe
★ 4.0k • written 2.9 years ago by
anasjamshed1994
• 0
0
votes
2
replies
1.6k
views
News:
Ensembl 103 has been released
biomaRt
ensembldb
Ensembl
ensemblVEP
Biomart
3.8 years ago • updated 3.6 years ago
mchakiachvili
▴ 20
0
votes
2
replies
1.3k
views
questions when installing 'Ensembl VEP' and R package 'ensemblVEP'
R
ensemblVEP
gene annotation
Variant Effect Predictor
Ensembl VEP
5.4 years ago
ycchang
• 0
2
votes
3
replies
1.7k
views
Error in VCF parsing with VariantAnnotation
software error
VariantAnnotation
ensemblVEP
updated 5.7 years ago by
Valerie Obenchain
★ 6.8k • written 5.7 years ago by
mumichae
▴ 20
2
votes
5
replies
2.5k
views
ensemblVEP: "Ensembl VEP is not installed in your path."
software error
ensemblVEP
updated 5.7 years ago by
Martin Morgan
25k • written 5.7 years ago by
patrick.turko
▴ 10
0
votes
4
replies
1.4k
views
ensemblVEP supported versions, and troubleshooting
ensemblVEP
updated 6.7 years ago by
shepherl
4.1k • written 6.7 years ago by
Janet Young
▴ 740
0
votes
0
replies
1.2k
views
error using ensemblVEP v88 when querying rs67418256 with basic(param_vep)$everything=TRUE
ensemblvep
7.5 years ago
mlrubio
• 0
0
votes
0
replies
1.8k
views
problem using ensemblVEP with GRC37
ensemblvep
grch37
7.5 years ago
mikko.arvas
• 0
0
votes
1
reply
1.0k
views
ensemblVEP problem with MySQL database
ensemblvep
8.3 years ago
clairelsimpson
▴ 10
2
votes
4
replies
1.5k
views
parseCSQToGRanges() : mcols are all factors, despite some numeric fields
ensemblVEP
updated 8.5 years ago by
Martin Morgan
25k • written 8.5 years ago by
kevin.rue
▴ 350
2
votes
3
replies
2.2k
views
ensemblVEP support for Ensembl API version 78
ensemblvep
updated 9.9 years ago by
Valerie Obenchain
★ 6.8k • written 9.9 years ago by
Moiz Bootwalla
▴ 50
0
votes
2
replies
2.4k
views
ensemblVEP, variant_effect_predictor versions and release schedule
Transcription
HapMap
PolyPhen
SIFT
convert
genomes
ensemblVEP
Transcription
HapMap
SIFT
updated 10.9 years ago by
Valerie Obenchain
★ 6.8k • written 10.9 years ago by
Thomas Sandmann
▴ 30
0
votes
0
replies
1.2k
views
ensemblVEP, variant_effect_predictor versions and release schedule
Cancer
MLInterfaces
bridge
ensemblVEP
AnnotationHub
Cancer
MLInterfaces
bridge
ensemblVEP
10.9 years ago
Valerie Obenchain
★ 6.8k
0
votes
0
replies
1.4k
views
zero-row result breaks select() on PolyPhen.Hsapiens.* and SIFT.Hsapiens.*
VariantAnnotation
Annotation
PolyPhen
SIFT
annotate
VariantAnnotation
ensemblVEP
Annotation
11.0 years ago
Valerie Obenchain
★ 6.8k
0
votes
5
replies
1.4k
views
ensemblVEP, variant_effect_predictor versions and release schedule
ensemblVEP
ensemblVEP
updated 11.2 years ago by
Valerie Obenchain
★ 6.8k • written 11.2 years ago by
Guest User
★ 13k
0
votes
5
replies
2.2k
views
ensemblVEP: passing on coverage / frequency information
Coverage
VariantTools
ensemblVEP
Coverage
VariantTools
ensemblVEP
updated 11.6 years ago by
Valerie Obenchain
★ 6.8k • written 11.6 years ago by
Guest User
★ 13k
19 results • Page
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Replies
Answer: Epic v2 Annotation CpG_maf source?
by
James W. MacDonald
67k
Those all come from dbSNP by way of UCSC. [See here][1], particularly lines 114 and onward. Here is no MAF for a CpG. The MAF is for the…
Comment: Deseq2 res Function
by
James W. MacDonald
67k
In addition to Mike's comment, do note that if you are generating a heatmap based on the set of significant genes, the direction of your co…
Answer: Struggle with the replicates of epic array data
by
James W. MacDonald
67k
You shouldn't be using beta values for a linear model that assumes a unimodal, untruncated distribution (beta values are strictly on (0-1) …
Comment: Identifying potentially associated gene set to drug response using GSVA
by
Robert Castelo
★ 3.4k
So, if I understand correctly, you derived GSVA scores from gene sets corresponding somehow to drugs in your RNA-seq data. Since GSVA score…
Answer: Deseq2 res Function
by
Michael Love
43k
> Does this mean the young and KO groups were numerators and denominators in the analysis, respectively? Read over the vignette and work…
Votes
Appropriate use of the function treat of the limma package
Comment: Is it recommended to analyze different tissues together when using edgeR
Answer: Deseq2 res Function
Answer: BiocNeighbours Utility for k-Nearest Neighbour Classification
Answer: ANOVA like approach of edgeR
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