User: Lin

gravatar for Lin
Lin30
Reputation:
30
Status:
New User
Location:
United States
Last seen:
4 years, 3 months ago
Joined:
5 years, 4 months ago
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Posts by Lin

<prev • 4 results • page 1 of 1 • next >
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Comment: C: getGEO GSEMatrix = TRUE error
... Hopefully this reply helps someone. Turned out the problem was the combination of getGEO and R. It was encoded in such a way that this particular FTP download was blocked even though proxy was already setup correctly. I didn't find a solution other than using wireless connection to download this. ...
written 4.3 years ago by Lin30
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Comment: C: getting sequence by combining reference and variants (fasta and vcf files)
... GATK FastaAlternateReferenceMaker select the allele randomly. There is no option to select the allele based on allelic depth. ...
written 4.3 years ago by Lin30
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getting sequence by combining reference and variants (fasta and vcf files)
... Is there a tool that will incorporate the variants into a reference genome based on the genotype information (GT info) and the allele depth (AD info)? So, for loci where there is a variant, the tool will look at the genotype, if it is heterozygous it will take allele with highest allelic depth and ...
vcf genome sequence mutation snp written 4.3 years ago by Lin30 • updated 4.3 years ago by WouterDeCoster45k
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getGEO GSEMatrix = TRUE error
... Dear Bioconductor users, I am having problems using GEOquery. It won't download GEO dataset and I am getting the following error: getGEO("GSE44281", GSEMatrix = TRUE); ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE44nnn/GSE44281/matrix/ Found 1 file(s) GSE44281_series_matrix.txt.gz trying URL 'ftp:/ ...
gsematrix geoquery written 5.4 years ago by Lin30 • updated 5.4 years ago by Sean Davis26k

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