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variantannotation
•
reset
2
votes
2
replies
1.5k
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Matching Variants Between Two VCF Objects
VariantAnnotation
written 3.4 years ago by
Dario Strbenac
★ 1.5k
2
votes
3
replies
1.1k
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
0
votes
2
replies
539
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
0
votes
5
replies
472
views
locateVariant from VariantAnnotation returns wrong results
VariantAnnotation
locateVariant
updated 4 months ago by
James W. MacDonald
65k • written 5 months ago by
nhaus
▴ 30
0
votes
0
replies
443
views
Variant Filtering on very large VCF files
VariantAnnotation
VariantFiltering
7 months ago
Bogdan
▴ 670
0
votes
0
replies
157
views
RFC: significant changes to ensemblVEP package
VariantAnnotation
ensemblVEP
3 months ago
Vincent J. Carey, Jr.
6.7k
0
votes
1
reply
142
views
Is random access by row index possible for an indexed VCF file?
Rsamtools
VariantAnnotation
updated 6 weeks ago by
James W. MacDonald
65k • written 6 weeks ago by
maltethodberg
▴ 170
0
votes
0
replies
77
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
14 days ago
Stevie Pederson
• 0
8 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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