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ensemblVEP
•
reset
0
votes
0
replies
350
views
RFC: significant changes to ensemblVEP package
VariantAnnotation
ensemblVEP
11 months ago
Vincent J. Carey, Jr.
6.7k
0
votes
1
reply
558
views
Differential express genes in one group across all time points
DESeq2
edgeR
BP4RNAseq
ensemblVEP
updated 20 months ago by
Michael Love
43k • written 20 months ago by
DHARMESH
• 0
2
votes
3
replies
2.1k
views
How to use a specific Bioconductor version in custom Dockerfile
singularity
ensemblVEP
docker
2.0 years ago
jtaylor-predicine
• 0
0
votes
1
reply
956
views
Ensembl REST API Endpoints
ensemblVEP
EnsDb.Hsapiens.v79
updated 3.0 years ago by
Kevin Blighe
★ 4.0k • written 3.0 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 5.8 years ago by
Valerie Obenchain
★ 6.8k • written 5.8 years ago by
mumichae
▴ 20
2
votes
5
replies
2.6k
views
ensemblVEP: "Ensembl VEP is not installed in your path."
software error
ensemblVEP
updated 5.8 years ago by
Martin Morgan
25k • written 5.8 years ago by
patrick.turko
▴ 10
0
votes
4
replies
1.5k
views
ensemblVEP supported versions, and troubleshooting
ensemblVEP
updated 6.8 years ago by
shepherl
4.1k • written 6.8 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
7.6 years ago
mlrubio
• 0
0
votes
0
replies
1.8k
views
problem using ensemblVEP with GRC37
ensemblvep
grch37
7.6 years ago
mikko.arvas
• 0
0
votes
1
reply
1.0k
views
ensemblVEP problem with MySQL database
ensemblvep
8.4 years ago
clairelsimpson
▴ 10
2
votes
4
replies
1.6k
views
parseCSQToGRanges() : mcols are all factors, despite some numeric fields
ensemblVEP
updated 8.6 years ago by
Martin Morgan
25k • written 8.6 years ago by
kevin.rue
▴ 350
2
votes
3
replies
2.2k
views
ensemblVEP support for Ensembl API version 78
ensemblvep
updated 10.0 years ago by
Valerie Obenchain
★ 6.8k • written 10.0 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 11.0 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
11.0 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
11.1 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 11.7 years ago by
Valerie Obenchain
★ 6.8k • written 11.7 years ago by
Guest User
★ 13k
19 results • Page
1 of 1
Recent ...
Replies
Comment: Cross-validation with multiple control subgroups in limma
by
Ali Barry
▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma
by
Gordon Smyth
52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
by
Robert Castelo
★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS
by
Aidan
▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
by
Michael Love
43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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Ali Barry
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gabriel.hoffman
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Jenny Drnevich
★ 2.0k
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martin.grigorov
▴ 10
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to
James W. MacDonald
67k
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