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VRanges
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894
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Formal class VRanges versus Large VRanges
somaticsignatures
vranges
readvcfasvranges
6.4 years ago
guillaume.dachy
• 0
3
votes
4
replies
2.0k
views
Problem when transforming Platypus vcf to VRanges
variantannotation
vcf
readvcf
vranges
updated 6.5 years ago by
Michael Lawrence
★ 11k • written 6.5 years ago by
david.mas
• 0
0
votes
2
replies
1.4k
views
Error: invalid class "VRanges" object
variantannotation
VRanges
R
Rle
updated 6.5 years ago by
Valerie Obenchain
★ 6.8k • written 6.5 years ago by
Jayendra Shinde
• 0
1
vote
2
replies
2.0k
views
Trouble while concatenating VRanges object ()
somaticsignatures
somaticsignatures package
readvcfasvranges
vranges
7.4 years ago • updated 7.3 years ago
guillaume.dachy
• 0
0
votes
3
replies
1.5k
views
about VRanges and filtering somatic variants
vranges
vcf to vranges
8.0 years ago
Bogdan
▴ 670
1
vote
4
replies
2.1k
views
Converting VCF to VRanges
somaticsignatures
vranges
updated 8.5 years ago by
Julian Gehring
★ 1.3k • written 8.5 years ago by
arsala521
▴ 10
1
vote
2
replies
1.7k
views
Combining GRange/VRange objects
granges
vranges
readvcfasvranges
somaticsignatures
updated 8.8 years ago by
Michael Lawrence
★ 11k • written 8.8 years ago by
jpluta26
• 0
3
votes
9
replies
2.4k
views
SomaticSignatures mutationContext (char ',') not in lookup table
SomaticSignatures mutationContext
VRanges
updated 9.4 years ago by
Julian Gehring
★ 1.3k • written 9.4 years ago by
tesa.severson
▴ 10
2
votes
3
replies
2.6k
views
Metadata Missing from vcf when reading in with readVcfAsVRanges
variantannotation
vranges
readvcf
readvcfasvranges
metadata
9.9 years ago
summerela
• 0
3
votes
5
replies
3.4k
views
Add Custom Annotations to Multi-Sample VCF with VariantAnnotation() package
variantannotation
granges
DNAStringSetList
findoverlaps
Vranges
9.9 years ago
summerela
• 0
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Comment: iam not able to do retrive data using GEOquery R package
by
James W. MacDonald
67k
Another alternative is to use the `GEOmetadb` package ([vignette here)][1], which will allow you to make queries to identify GEO datasets t…
Answer: iam not able to do retrive data using GEOquery R package
by
James W. MacDonald
67k
Before you try to use a function, you should read the help page to ensure that you are using the correct argument type. As an example, here…
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
by
James W. MacDonald
67k
It's not the version control in R/Bioconductor though. It's the version of the genome. OP used Ensembl build 113 to align and then noted th…
Comment: Why did PCA plots look exactly the same after adjusting for batch covariate in D
by
Quang
▴ 10
Also, Michael, when I used SVA in addition, so I have the `design = ~ Date_lysed + SV1 + condition_subset`, do I just set `mat_corrected <-…
Comment: Differential variability modelling with vst() expression
by
Michael Love
43k
See Gordon's reply below for an implementation you can use directly.
Votes
Answer: Differential variability modelling with vst() expression
Answer: Differential variability modelling with vst() expression
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
Answer: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
Comment: Why did PCA plots look exactly the same after adjusting for batch covariate in D
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