User: johntimcham

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Posts by johntimcham

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Comment: C: Unable to access ensembl biomart archives via R
... What version of R and biomaRt are you using? I am on: R version 3.5.1 (2018-07-02) biomaRt_2.41.4 edit: I tried updating my biomart, which resulted in it being replace by biomaRt_2.38.0. I am on bioconductor version 3.8 because my university's compute cluster hasn't installed R 3.6 yet. I'm not ...
written 3 months ago by johntimcham0
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Unable to access ensembl biomart archives via R
... > EDIT: I tried updating biomaRt, which replaced it with version 2.38.0 > (see my response to genomax). After restarting RStudio the error has > vanished. Perhaps there was an issue with some dependency. I'm trying to access biomart version 93 (human) because this happens to be the ver ...
R biomart ensembl written 3 months ago by johntimcham0 • updated 3 months ago by Mike Smith1.4k
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Ensembl Variation REST API Phased Haplotype?
... I am using the Ensembl REST API to access variation data for a selection of SNPs. The output for each allele is in the form "G|A" for each rs# that I provide. Suppose for two SNPs the output is "G|C" and "A|T". Does this mean that one chromosome has the G and A variants while the other chromosome ha ...
ensembl haplotype rest api 1000 genomes written 2.3 years ago by johntimcham0
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Designating regulatory region threshold
... Hello, I am attempting to evaluate population-specific allele frequencies of gene variants for a set of genes. Is there any reason to adjust my window beyond the generic +- 5kb that Ensembl uses by default? Thanks ...
gene ensembl regulation variation promoter written 2.4 years ago by johntimcham0 • updated 2.4 years ago by Emily_Ensembl19k

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