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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409
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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
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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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779
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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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
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3
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1.4k
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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
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5
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2.2k
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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
6.9 years ago mlrubio • 0
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1.7k
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problem using ensemblVEP with GRC37
ensemblvep grch37
7.0 years ago mikko.arvas • 0
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876
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ensemblVEP problem with MySQL database
ensemblvep
7.7 years ago clairelsimpson ▴ 10
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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
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ensemblVEP support for Ensembl API version 78
ensemblvep
updated 9.3 years ago by ★ 6.8k • written 9.4 years ago by ▴ 50
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2
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2.2k
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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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1.1k
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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
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ensemblVEP: passing on coverage / frequency information
Coverage VariantTools ensemblVEP Coverage VariantTools ensemblVEP
updated 11.0 years ago by ★ 6.8k • written 11.0 years ago by ★ 13k
19 results • Page 1 of 1
Recent ...
Replies
Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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