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readVcf
•
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0
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0
replies
457
views
VariantAnnotation::readVcf incorrectly processes GATK Mutect2 vcf INFO field AS_SB_TABLE
vcf
AS_SB_TABLE
readVcf
Mutect2
VariantAnnotation
14 months ago
therealgenna
• 0
1
vote
12
replies
2.9k
views
readVcf does not recognize tabix index
VariantAnnotation
readvcf
tabix
updated 3.0 years ago by
Vincent J. Carey, Jr.
6.7k • written 3.1 years ago by
naive
• 0
0
votes
2
replies
1.2k
views
readVCF requires the argument "genome". What does it stand for?
Genome
readVcf
VariantAnnotation
3.1 years ago
naive
• 0
3
votes
4
replies
1.7k
views
Problem when transforming Platypus vcf to VRanges
variantannotation
vcf
readvcf
vranges
updated 5.8 years ago by
Michael Lawrence
★ 11k • written 5.8 years ago by
david.mas
• 0
2
votes
5
replies
2.6k
views
VariantAnnotation: Error with ScanVcfParam
variantannotation
vcf
readvcf
filtervcf
scanvcfparam
6.7 years ago
Didi
▴ 10
1
vote
4
replies
2.1k
views
cannot allocate memory?
readVcf
updated 7.0 years ago by
Martin Morgan
25k • written 7.0 years ago by
Haiying.Kong
▴ 110
0
votes
2
replies
1.0k
views
does readVcf mistakenly ignore ploidy for missing genotypes?
readvcf
gt
missing
VariantAnnotation
7.1 years ago
TimothéeFlutre
▴ 80
2
votes
4
replies
1.9k
views
Best way to create a VRanges object from a large VCF file?
variantannotation
readvcf
readvcfasvranges
vcf
updated 7.3 years ago by
Michael Lawrence
★ 11k • written 7.3 years ago by
ruben.drews
• 0
0
votes
2
replies
1.6k
views
Subsetting info columns from a VCF and getting rsID for some row names?
R
variantannotation
vcf
scanvcfparam
readvcf
updated 7.9 years ago by
Michael Lawrence
★ 11k • written 7.9 years ago by
emily.mccann
• 0
0
votes
2
replies
1.5k
views
Duplicated rows in readVcf output
variantannotation
readvcf
updated 8.0 years ago by
Valerie Obenchain
★ 6.8k • written 8.0 years ago by
nicolas.o.rode
• 0
0
votes
1
reply
1.5k
views
mutational signatures problems
bsgenome
readvcf
tcga
annotation
somaticsignatures
updated 8.1 years ago by
Julian Gehring
★ 1.3k • written 8.1 years ago by
jolligoodfellow
• 0
0
votes
4
replies
2.7k
views
How to import vcf with multi sample?
vcf
readvcf
readvcfasvranges
8.3 years ago
Marcin Grzybowski
• 0
1
vote
1
reply
1.1k
views
Suppressing the ID value from writeVcf
readvcf
writevcf
updated 8.4 years ago by
Valerie Obenchain
★ 6.8k • written 8.4 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 8.7 years ago by
Valerie Obenchain
★ 6.8k • written 8.7 years ago by
Simon Coetzee
▴ 50
2
votes
9
replies
2.7k
views
ReadVCF not reading samples
readvcf
vcf
variantannotation
8.9 years ago
askates
▴ 10
0
votes
21
replies
4.3k
views
VariantAnnotation Errors and void outputs
variantannotation
readvcf
8.9 years ago
pifferdavide
• 0
1
vote
5
replies
4.3k
views
Converting a DNAStringSetList to characters quickly
readVcf
DNAStringSet
DNAStringSetList
variantannotation
readvcf
9.0 years ago
dan.gatti
• 0
0
votes
2
replies
2.1k
views
Error reading vcf converted from bed file
readvcf
plink
file conversion
bed
bioc-devel
9.1 years ago
mjsduncan
• 0
2
votes
3
replies
2.2k
views
Metadata Missing from vcf when reading in with readVcfAsVRanges
variantannotation
vranges
readvcf
readvcfasvranges
metadata
9.2 years ago
summerela
• 0
1
vote
12
replies
2.8k
views
VariantAnnotation: no method for function 'path' for signature 'character'
variantannotation
readvcf
readgt
updated 9.4 years ago by
Valerie Obenchain
★ 6.8k • written 9.4 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
9.4 years ago
jls2282
• 0
2
votes
3
replies
1.3k
views
readVcf skipping CS field in INFO
variantannotation
readVcf
updated 9.5 years ago by
Valerie Obenchain
★ 6.8k • written 9.5 years ago by
Peter Hickey
▴ 710
0
votes
5
replies
1.7k
views
VariantAnnotation VCF read error
variantannotation
readvcf
updated 9.5 years ago by
Valerie Obenchain
★ 6.8k • written 9.5 years ago by
JK
▴ 10
23 results • Page
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Comment: Error in champ.load(): The following specified files do not exist
by
Basti
▴ 760
The error stems from the Basename column, please see solution here : https://support.bioconductor.org/p/p132482/
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Gordon Smyth
50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
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Gordon Smyth
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In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
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I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups.
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Chris
• 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with psychology doctor who treat Alzheimer patients and they don'…
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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