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readvcf
•
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0
votes
0
replies
943
views
VariantAnnotation::readVcf incorrectly processes GATK Mutect2 vcf INFO field AS_SB_TABLE
vcf
AS_SB_TABLE
readVcf
Mutect2
VariantAnnotation
2.7 years ago
therealgenna
• 0
1
vote
12
replies
4.7k
views
readVcf does not recognize tabix index
VariantAnnotation
readvcf
tabix
updated 4.6 years ago by
Vincent J. Carey, Jr.
6.7k • written 4.6 years ago by
naive
• 0
0
votes
2
replies
2.0k
views
readVCF requires the argument "genome". What does it stand for?
Genome
readVcf
VariantAnnotation
4.6 years ago
naive
• 0
3
votes
4
replies
2.3k
views
Problem when transforming Platypus vcf to VRanges
variantannotation
vcf
readvcf
vranges
updated 7.3 years ago by
Michael Lawrence
★ 11k • written 7.3 years ago by
david.mas
• 0
2
votes
5
replies
3.3k
views
VariantAnnotation: Error with ScanVcfParam
variantannotation
vcf
readvcf
filtervcf
scanvcfparam
8.2 years ago
Didi
▴ 10
1
vote
4
replies
2.8k
views
cannot allocate memory?
readVcf
updated 8.5 years ago by
Martin Morgan
25k • written 8.5 years ago by
Haiying.Kong
▴ 110
0
votes
2
replies
1.4k
views
does readVcf mistakenly ignore ploidy for missing genotypes?
readvcf
gt
missing
VariantAnnotation
8.7 years ago
TimothéeFlutre
▴ 80
2
votes
4
replies
2.6k
views
Best way to create a VRanges object from a large VCF file?
variantannotation
readvcf
readvcfasvranges
vcf
updated 8.8 years ago by
Michael Lawrence
★ 11k • written 8.8 years ago by
ruben.drews
• 0
0
votes
2
replies
2.1k
views
Subsetting info columns from a VCF and getting rsID for some row names?
R
variantannotation
vcf
scanvcfparam
readvcf
updated 9.4 years ago by
Michael Lawrence
★ 11k • written 9.4 years ago by
emily.mccann
• 0
0
votes
2
replies
2.0k
views
Duplicated rows in readVcf output
variantannotation
readvcf
updated 9.5 years ago by
Valerie Obenchain
★ 6.8k • written 9.5 years ago by
nicolas.o.rode
• 0
0
votes
2
replies
2.1k
views
mutational signatures problems
bsgenome
readvcf
tcga
annotation
somaticsignatures
updated 13 months ago by
Danyiel
• 0 • written 9.6 years ago by
jolligoodfellow
• 0
0
votes
4
replies
3.2k
views
How to import vcf with multi sample?
vcf
readvcf
readvcfasvranges
9.8 years ago
Marcin Grzybowski
• 0
1
vote
1
reply
1.4k
views
Suppressing the ID value from writeVcf
readvcf
writevcf
updated 9.9 years ago by
Valerie Obenchain
★ 6.8k • written 9.9 years ago by
fongchunchan
▴ 30
2
votes
1
reply
2.0k
views
readVCF with 1000 genomes data from 20130502 fails to return genotype information
readvcf
vcf
tabix
updated 10.3 years ago by
Valerie Obenchain
★ 6.8k • written 10.3 years ago by
Simon Coetzee
▴ 50
2
votes
9
replies
3.7k
views
ReadVCF not reading samples
readvcf
vcf
variantannotation
10.4 years ago
askates
▴ 10
0
votes
21
replies
5.7k
views
VariantAnnotation Errors and void outputs
variantannotation
readvcf
10.4 years ago
pifferdavide
• 0
1
vote
5
replies
5.1k
views
Converting a DNAStringSetList to characters quickly
readVcf
DNAStringSet
DNAStringSetList
variantannotation
readvcf
10.5 years ago
dan.gatti
• 0
0
votes
2
replies
2.7k
views
Error reading vcf converted from bed file
readvcf
plink
file conversion
bed
bioc-devel
10.6 years ago
mjsduncan
• 0
2
votes
3
replies
3.0k
views
Metadata Missing from vcf when reading in with readVcfAsVRanges
variantannotation
vranges
readvcf
readvcfasvranges
metadata
10.7 years ago
summerela
• 0
1
vote
12
replies
3.5k
views
VariantAnnotation: no method for function 'path' for signature 'character'
variantannotation
readvcf
readgt
updated 10.9 years ago by
Valerie Obenchain
★ 6.8k • written 10.9 years ago by
Kipper Fletez-Brant
▴ 150
0
votes
1
reply
1.8k
views
readVCF (VariantAnnotation) problem with mismatched header and info fields in vcf file
annotation
vcf
readvcf
variantannotation
10.9 years ago
jls2282
• 0
2
votes
3
replies
1.7k
views
readVcf skipping CS field in INFO
variantannotation
readVcf
updated 11.0 years ago by
Valerie Obenchain
★ 6.8k • written 11.0 years ago by
Peter Hickey
▴ 760
0
votes
5
replies
2.2k
views
VariantAnnotation VCF read error
variantannotation
readvcf
updated 11.0 years ago by
Valerie Obenchain
★ 6.8k • written 11.0 years ago by
JK
▴ 10
23 results • Page
1 of 1
Recent ...
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by
ATpoint
★ 5.0k
You sure will find online tutorials on regression models / machine learning classifiers. The support site is for help with Bioconductor. Ch…
Comment: Using DESeq2 for age prediction
by
picasa1983
• 0
Thanks ! Do you have any idea how to do that ?
Answer: Using DESeq2 for age prediction
by
ATpoint
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The package has no such inbuilt function but you are free to use the vst (or any normalized) counts to train a regression model or classifi…
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James W. MacDonald
68k
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
dan.gatti
• 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
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