User: micahgearhart

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United States
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6 years, 2 months ago
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Posts by micahgearhart

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Comment: C: Querying the UCSC Genome Browser for DNA sequences (large collection of data)
... If the sequences are all from the same genome I would recommend downloading the 2bit file for the genome and using a command line package like `twoBitToFa`. For hg19, download this file (778 MB) and access it with this linux software. If you'd prefer to do it in R, check out the BSgenome and DNAst ...
written 6.2 years ago by micahgearhart40 • updated 13 months ago by _r_am31k
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Answer: A: JASPAR, TFs and their target genes
... Check out MotifDb. Something like `query(MotifDb, 'Mmusculus')` should return the list you want. This code will work for one gene and one promoter for Drosophila: txdb <- makeTranscriptDbFromBiomart(biomart="ensembl",dataset="dmelanogaster_gene_ensembl") tx <- transcriptsBy(txdb, by ...
written 6.5 years ago by micahgearhart40 • updated 10 months ago by _r_am31k
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Answer: A: How to resize a GenomicRange objects centered on a DNA motif
... This function returns an aligned GRanges object based on matchPattern or will also work with matchPWM. It's a little slow because it has to retrieve the DNA sequence for each range but I wanted to make sure there was only one site under each peak. returnAlignedGR <- function(gr,pattern,width ...
written 6.6 years ago by micahgearhart40 • updated 11 months ago by _r_am31k

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