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readVcf
•
reset
1
vote
5
replies
3.2k
views
Converting a DNAStringSetList to characters quickly
readVcf
DNAStringSet
DNAStringSetList
variantannotation
readvcf
7.1 years ago
dan.gatti
• 0
0
votes
21
replies
2.7k
views
VariantAnnotation Errors and void outputs
variantannotation
readvcf
7.0 years ago
pifferdavide
• 0
1
vote
12
replies
2.2k
views
VariantAnnotation: no method for function 'path' for signature 'character'
variantannotation
readvcf
readgt
updated 7.5 years ago by
Valerie Obenchain
★ 6.7k • written 7.5 years ago by
Kipper Fletez-Brant
▴ 150
0
votes
4
replies
1.9k
views
How to import vcf with multi sample?
vcf
readvcf
readvcfasvranges
6.4 years ago
Marcin Grzybowski
• 0
2
votes
9
replies
1.8k
views
ReadVCF not reading samples
readvcf
vcf
variantannotation
7.0 years ago
askates
▴ 10
2
votes
5
replies
1.8k
views
VariantAnnotation: Error with ScanVcfParam
variantannotation
vcf
readvcf
filtervcf
scanvcfparam
4.8 years ago
Didi
▴ 10
2
votes
3
replies
1.5k
views
Metadata Missing from vcf when reading in with readVcfAsVRanges
variantannotation
vranges
readvcf
readvcfasvranges
metadata
7.3 years ago
summerela
• 0
1
vote
4
replies
1.4k
views
cannot allocate memory?
readVcf
updated 5.1 years ago by
Martin Morgan
25k • written 5.1 years ago by
Haiying.Kong
▴ 110
0
votes
2
replies
1.4k
views
Error reading vcf converted from bed file
readvcf
plink
file conversion
bed
bioc-devel
7.2 years ago
mjsduncan
• 0
0
votes
5
replies
1.2k
views
VariantAnnotation VCF read error
variantannotation
readvcf
updated 7.6 years ago by
Valerie Obenchain
★ 6.7k • written 7.6 years ago by
JK
▴ 10
0
votes
1
reply
1.2k
views
readVCF (VariantAnnotation) problem with mismatched header and info fields in vcf file
annotation
vcf
readvcf
variantannotation
7.5 years ago
jls2282
• 0
2
votes
4
replies
1.1k
views
Best way to create a VRanges object from a large VCF file?
variantannotation
readvcf
readvcfasvranges
vcf
updated 5.4 years ago by
Michael Lawrence
11k • written 5.4 years ago by
ruben.drews
• 0
0
votes
1
reply
1.1k
views
mutational signatures problems
bsgenome
readvcf
tcga
annotation
somaticsignatures
updated 6.2 years ago by
Julian Gehring
★ 1.3k • written 6.2 years ago by
jolligoodfellow
• 0
0
votes
2
replies
1.0k
views
Subsetting info columns from a VCF and getting rsID for some row names?
R
variantannotation
vcf
scanvcfparam
readvcf
updated 6.0 years ago by
Michael Lawrence
11k • written 6.0 years ago by
emily.mccann
• 0
0
votes
2
replies
991
views
Duplicated rows in readVcf output
variantannotation
readvcf
updated 6.1 years ago by
Valerie Obenchain
★ 6.7k • written 6.1 years ago by
nicolas.o.rode
• 0
1
vote
12
replies
952
views
readVcf does not recognize tabix index
VariantAnnotation
readvcf
tabix
updated 14 months ago by
Vincent J. Carey, Jr.
6.6k • written 14 months ago by
naive
• 0
2
votes
1
reply
940
views
readVCF with 1000 genomes data from 20130502 fails to return genotype information
readvcf
vcf
tabix
updated 6.9 years ago by
Valerie Obenchain
★ 6.7k • written 6.9 years ago by
Simon Coetzee
▴ 50
2
votes
3
replies
921
views
readVcf skipping CS field in INFO
variantannotation
readVcf
updated 7.6 years ago by
Valerie Obenchain
★ 6.7k • written 7.6 years ago by
Peter Hickey
▴ 550
3
votes
4
replies
830
views
Problem when transforming Platypus vcf to VRanges
variantannotation
vcf
readvcf
vranges
updated 3.9 years ago by
Michael Lawrence
11k • written 3.9 years ago by
david.mas
• 0
1
vote
1
reply
706
views
Suppressing the ID value from writeVcf
readvcf
writevcf
updated 6.5 years ago by
Valerie Obenchain
★ 6.7k • written 6.5 years ago by
fongchunchan
▴ 30
0
votes
2
replies
696
views
does readVcf mistakenly ignore ploidy for missing genotypes?
readvcf
gt
missing
VariantAnnotation
5.2 years ago
TimothéeFlutre
▴ 80
0
votes
2
replies
280
views
readVCF requires the argument "genome". What does it stand for?
Genome
readVcf
VariantAnnotation
14 months ago
naive
• 0
22 results • Page
1 of 1
Recent ...
Replies
Comment: Italicise
by
Pau
• 0
They're the same: example of the vignette: "italic('VCAM1')" and result from my data: "italic('CARS1')" As I am running against time be…
Comment: Can Differential Isoform expression analysis can be performed using DESeq2 packa
by
priyanka.m
• 0
Thank you for the suggestions. I will try to compare my results and accordingly interpret the two.
Answer: [sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
by
wahaha
• 0
I found the reason, because some gene expression levels are 0 in all samples. you can add these code to check the data: >exp_mean <- appl…
Answer: DESeq2 how to specify contrast to test difference of differences
by
Nicole
• 0
The comment from @mikelove about specifying numeric contrasts answered my question. This code is not standalone, but I will leave it here i…
Comment: DESeq2 how to specify contrast to test difference of differences
by
Nicole
• 0
Thank you, @mikelove - that did it! The results make sense now. From my original post, could you clarify what the `group1w.sexfemale` contr…
Votes
Answer: DESeq2 how to specify contrast to test difference of differences
Comment: DESeq2 how to specify contrast to test difference of differences
Answer: Confused about the design matrix in edgeR: How to tell R to consider one level a
Answer: biomaRt error unable to fix: need help troubleshooting
Answer: edgeR : results from goana and kegga functions show opposite sig. p-value
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