Showing : ensemblvep • reset
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RFC: significant changes to ensemblVEP package
VariantAnnotation ensemblVEP
3 months ago Vincent J. Carey, Jr. 6.7k
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1
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412
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Differential express genes in one group across all time points
DESeq2 edgeR BP4RNAseq ensemblVEP
updated 12 months ago by 41k • written 12 months ago by • 0
2
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3
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1.5k
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How to use a specific Bioconductor version in custom Dockerfile
singularity ensemblVEP docker
16 months ago jtaylor-predicine • 0
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1
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781
views
Ensembl REST API Endpoints
ensemblVEP EnsDb.Hsapiens.v79
updated 2.3 years ago by ★ 3.9k • written 2.3 years ago by • 0
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2
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1.3k
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News: Ensembl 103 has been released
biomaRt ensembldb Ensembl ensemblVEP Biomart
3.2 years ago • updated 3.0 years ago mchakiachvili ▴ 20
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2
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1.1k
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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
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3
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1.4k
views
Error in VCF parsing with VariantAnnotation
software error VariantAnnotation ensemblVEP
updated 5.1 years ago by ★ 6.8k • written 5.1 years ago by ▴ 20
2
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5
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2.2k
views
ensemblVEP: "Ensembl VEP is not installed in your path."
software error ensemblVEP
updated 5.1 years ago by 25k • written 5.1 years ago by ▴ 10
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4
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1.2k
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ensemblVEP supported versions, and troubleshooting
ensemblVEP
updated 6.1 years ago by 3.8k • written 6.1 years ago by ▴ 740
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1.1k
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error using ensemblVEP v88 when querying rs67418256 with basic(param_vep)$everything=TRUE
ensemblvep
7.0 years ago mlrubio • 0
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1.7k
views
problem using ensemblVEP with GRC37
ensemblvep grch37
7.0 years ago mikko.arvas • 0
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1
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878
views
ensemblVEP problem with MySQL database
ensemblvep
7.7 years ago clairelsimpson ▴ 10
2
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4
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1.4k
views
parseCSQToGRanges() : mcols are all factors, despite some numeric fields
ensemblVEP
updated 8.0 years ago by 25k • written 8.0 years ago by ▴ 350
2
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3
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2.1k
views
ensemblVEP support for Ensembl API version 78
ensemblvep
updated 9.4 years ago by ★ 6.8k • written 9.4 years ago by ▴ 50
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votes
2
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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 ★ 6.8k • written 10.3 years ago by ▴ 30
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0
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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
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1.2k
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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
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5
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1.3k
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ensemblVEP, variant_effect_predictor versions and release schedule
ensemblVEP ensemblVEP
updated 10.6 years ago by ★ 6.8k • written 10.6 years ago by ★ 13k
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5
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2.0k
views
ensemblVEP: passing on coverage / frequency information
Coverage VariantTools ensemblVEP Coverage VariantTools ensemblVEP
updated 11.1 years ago by ★ 6.8k • written 11.1 years ago by ★ 13k
19 results • Page 1 of 1
Recent ...
Replies
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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