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CustomProDB InputVcf() - Issue getting the GRanges INDEL object from VCF file
vcf
snv
gatk
customprodb
inputvcf
4.8 years ago
Elena.M
• 0
0
votes
1
reply
2.1k
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Adaptive Lasso and CrossValidation for SNV selection
adaptive-lasso
snv
biomarkers
cv
glmnet
7.4 years ago
crichard
• 0
1
vote
2
replies
1.0k
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Locating enhancers that are mutated
snv
granges
genomicranges
variantannotation
indel
updated 7.7 years ago by
Michael Lawrence
★ 11k • written 7.7 years ago by
addyS
• 0
3
votes
3
replies
2.2k
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about VCF and BAM files
SNV
BAM
8.0 years ago
Bogdan
▴ 670
4 results • Page
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Answer: rlog transformation
by
Michael Love
41k
It is dependent on the other samples in the dataset.
Answer: ONT long-read RNA sequencing - data analysis options
by
Michael Love
41k
*"This worked really well for brain but has not work as well for lung as I get #N/A for many padj"* See the vignette for the cause of th…
Answer: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
Michael Love
41k
Starting from the very top, do you understand the error? You need to provide sample info that matches 1-to-1 the columns of the counts matr…
Answer: covariate with negative and positive values
by
Michael Love
41k
Not a problem. However, if the values are very large (eg 1e6) or very small (eg 1e-6), it's a good idea to center and scale the variable…
Comment: FilterByExpr low counts with small sample size
by
Jonathan
▴ 10
Usually I run `voomLmFit`, although in order to create the mean-variance trend plots for this particular post, I ran `voom`; I've checked -…
Votes
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Using GRanges and IRanges to simply get all chromosome data
A: Using GRanges and IRanges to simply get all chromosome data
Comment: Reading huge bismark coverage files using bbseq::read.bismark
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