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readvcf
•
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0
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0
replies
549
views
VariantAnnotation::readVcf incorrectly processes GATK Mutect2 vcf INFO field AS_SB_TABLE
vcf
AS_SB_TABLE
readVcf
Mutect2
VariantAnnotation
16 months ago
therealgenna
• 0
1
vote
12
replies
3.2k
views
readVcf does not recognize tabix index
VariantAnnotation
readvcf
tabix
updated 3.3 years ago by
Vincent J. Carey, Jr.
6.7k • written 3.3 years ago by
naive
• 0
0
votes
2
replies
1.4k
views
readVCF requires the argument "genome". What does it stand for?
Genome
readVcf
VariantAnnotation
3.3 years ago
naive
• 0
3
votes
4
replies
1.8k
views
Problem when transforming Platypus vcf to VRanges
variantannotation
vcf
readvcf
vranges
updated 6.0 years ago by
Michael Lawrence
★ 11k • written 6.0 years ago by
david.mas
• 0
2
votes
5
replies
2.7k
views
VariantAnnotation: Error with ScanVcfParam
variantannotation
vcf
readvcf
filtervcf
scanvcfparam
6.9 years ago
Didi
▴ 10
1
vote
4
replies
2.2k
views
cannot allocate memory?
readVcf
updated 7.2 years ago by
Martin Morgan
25k • written 7.2 years ago by
Haiying.Kong
▴ 110
0
votes
2
replies
1.1k
views
does readVcf mistakenly ignore ploidy for missing genotypes?
readvcf
gt
missing
VariantAnnotation
7.3 years ago
TimothéeFlutre
▴ 80
2
votes
4
replies
2.0k
views
Best way to create a VRanges object from a large VCF file?
variantannotation
readvcf
readvcfasvranges
vcf
updated 7.5 years ago by
Michael Lawrence
★ 11k • written 7.5 years ago by
ruben.drews
• 0
0
votes
2
replies
1.7k
views
Subsetting info columns from a VCF and getting rsID for some row names?
R
variantannotation
vcf
scanvcfparam
readvcf
updated 8.1 years ago by
Michael Lawrence
★ 11k • written 8.1 years ago by
emily.mccann
• 0
0
votes
2
replies
1.6k
views
Duplicated rows in readVcf output
variantannotation
readvcf
updated 8.2 years ago by
Valerie Obenchain
★ 6.8k • written 8.2 years ago by
nicolas.o.rode
• 0
0
votes
1
reply
1.6k
views
mutational signatures problems
bsgenome
readvcf
tcga
annotation
somaticsignatures
updated 8.3 years ago by
Julian Gehring
★ 1.3k • written 8.3 years ago by
jolligoodfellow
• 0
0
votes
4
replies
2.8k
views
How to import vcf with multi sample?
vcf
readvcf
readvcfasvranges
8.5 years ago
Marcin Grzybowski
• 0
1
vote
1
reply
1.1k
views
Suppressing the ID value from writeVcf
readvcf
writevcf
updated 8.6 years ago by
Valerie Obenchain
★ 6.8k • written 8.6 years ago by
fongchunchan
▴ 30
2
votes
1
reply
1.4k
views
readVCF with 1000 genomes data from 20130502 fails to return genotype information
readvcf
vcf
tabix
updated 9.0 years ago by
Valerie Obenchain
★ 6.8k • written 9.0 years ago by
Simon Coetzee
▴ 50
2
votes
9
replies
2.8k
views
ReadVCF not reading samples
readvcf
vcf
variantannotation
9.1 years ago
askates
▴ 10
0
votes
21
replies
4.4k
views
VariantAnnotation Errors and void outputs
variantannotation
readvcf
9.1 years ago
pifferdavide
• 0
1
vote
5
replies
4.4k
views
Converting a DNAStringSetList to characters quickly
readVcf
DNAStringSet
DNAStringSetList
variantannotation
readvcf
9.2 years ago
dan.gatti
• 0
0
votes
2
replies
2.2k
views
Error reading vcf converted from bed file
readvcf
plink
file conversion
bed
bioc-devel
9.3 years ago
mjsduncan
• 0
2
votes
3
replies
2.3k
views
Metadata Missing from vcf when reading in with readVcfAsVRanges
variantannotation
vranges
readvcf
readvcfasvranges
metadata
9.4 years ago
summerela
• 0
1
vote
12
replies
2.9k
views
VariantAnnotation: no method for function 'path' for signature 'character'
variantannotation
readvcf
readgt
updated 9.6 years ago by
Valerie Obenchain
★ 6.8k • written 9.6 years ago by
Kipper Fletez-Brant
▴ 150
0
votes
1
reply
1.5k
views
readVCF (VariantAnnotation) problem with mismatched header and info fields in vcf file
annotation
vcf
readvcf
variantannotation
9.6 years ago
jls2282
• 0
2
votes
3
replies
1.3k
views
readVcf skipping CS field in INFO
variantannotation
readVcf
updated 9.7 years ago by
Valerie Obenchain
★ 6.8k • written 9.7 years ago by
Peter Hickey
▴ 740
0
votes
5
replies
1.7k
views
VariantAnnotation VCF read error
variantannotation
readvcf
updated 9.7 years ago by
Valerie Obenchain
★ 6.8k • written 9.7 years ago by
JK
▴ 10
23 results • Page
1 of 1
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Replies
Comment: Ranking the GSEA Results
by
Lluís Revilla Sancho
▴ 730
You can have the ranking without the cutoff. If you don't keep any gene set after the cutoff then there is nothing to rank as you said, so…
Answer: Create a Graph w/ Only the Genes Interaction
by
Antonio
• 0
Thank you all, I solved my issue by creating a for loop. Cheers!
Comment: Ranking the GSEA Results
by
alserg
▴ 270
Apparently, it sends a notification to the developer on a new message after the tags were updated :) but not the change of tags itself
Comment: Ranking the GSEA Results
by
alserg
▴ 270
Where did you see ranking of genes by `log2FC * (-log10 p-value)`? I don't think I ever saw one and not sure what it should achieve. Aren't…
Comment: Trouble Installing DADA2 (warning: R new user)
by
shepherl
3.9k
As far as this ERROR for Bioc requires R version, Bioconductor is closely tied to an R release. Depending if you tried to use a premade s…
Votes
Comment: Ranking the GSEA Results
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
Comment: How to get the DMR?
Answer: Using both voom and removeBatchEffect, will they double adjust the data or is it
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