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variantannotation
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Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
7 days ago
Stevie Pederson
• 0
0
votes
1
reply
132
views
Is random access by row index possible for an indexed VCF file?
Rsamtools
VariantAnnotation
updated 5 weeks ago by
James W. MacDonald
65k • written 5 weeks ago by
maltethodberg
▴ 170
0
votes
0
replies
148
views
RFC: significant changes to ensemblVEP package
VariantAnnotation
ensemblVEP
3 months ago
Vincent J. Carey, Jr.
6.7k
0
votes
5
replies
459
views
locateVariant from VariantAnnotation returns wrong results
VariantAnnotation
locateVariant
updated 4 months ago by
James W. MacDonald
65k • written 4 months ago by
nhaus
▴ 30
0
votes
0
replies
429
views
Variant Filtering on very large VCF files
VariantAnnotation
VariantFiltering
6 months ago
Bogdan
▴ 670
2
votes
2
replies
1.4k
views
Matching Variants Between Two VCF Objects
VariantAnnotation
written 3.4 years ago by
Dario Strbenac
★ 1.5k
0
votes
2
replies
526
views
Docker usage with Trio Bioconductor Package
VariantAnnotation
docker
trio
updated 11 months ago by
ATpoint
★ 4.0k • written 11 months ago by
sethberke
• 0
2
votes
3
replies
1.0k
views
readVcf(remoteFile, "hg19", "region") works on macos, fails on linux and in docker
open.BcfFile
VariantAnnotation
updated 3 months ago by
Alex
• 0 • written 2.8 years ago by
Paul Shannon
▴ 470
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Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Chris
• 0
Hi Robert, If I don't want to use all pathway in c2 gene set but only a few pathways of interested, how can I do that? So we try to get a …
Comment: How to retrieve detailed regression results from deseq2
by
Weiqian
▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size
by
Jonathan
▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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