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  • Bioconductor - GenomicRanges
    The GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome More specialized containers for representing and manipulating short alignments against a reference genome, or a matrix-like summarization of an experiment, are defined in the GenomicAlignments and
  • GenomicRanges HOWTOs
    A large BAM file can be iterated through in chunks by setting ayieldSizeon theBam- Fileobject As sample data we use thepasillaBamSubsetdata package described in the
  • Using the Bioconductor GenomicsRanges package - GitHub Pages
    From the introductory article for GenomicRanges: The GenomicRanges package serves as the foundation for representing genomic locations within the Bioconductor project
  • Genomic ranges: GRanges - GitHub Pages
    In this lecture note, we demonstrate how to specify regions of the genome (genomic ranges) in R Bioconductor We will make use of the GenomicRanges package and the GRanges object defined by this package The package also provides a number of methods that work on this type of object
  • GenomicRanges HOWTOs - MIT - Massachusetts Institute of Technology
    File object As sample data we use the pasillaBamSubset data package described in the introduction > library(pasillaBamSubset) > un1 <- untreated1_chr4() > bf <- BamFile(un1, yieldSize=100000) Iteration through a BAM file requires that the file be opened, repeatedly queried inside a loop,thenclosed
  • 6. 1 Operations on genomic intervals with GenomicRanges package . . .
    GRanges (from GenomicRanges package) is the main object that holds the genomic intervals and extra information about those intervals Here we will show how to create one
  • Looping over entries of a GRanges object - Bioconductor
    Hi, Is there a fast way of looping over extracting the entries of a 'GRanges' object individually? Due to the complex structure of a GRanges object, a simple solution like library (GenomicRanges) n = 1e4 gr = GRanges (1, IRanges (1:n, width = 1)) for (i in seq_along (gr)) { x = gr [i] ## more complex code acting on 'x' } takes notably long
  • GenomicRanges HOWTOs - Bioconductor
    File object As sample data we use the pasillaBamSubset data package described in the introduction > library(pasillaBamSubset) > un1 <- untreated1_chr4() > bf <- BamFile(un1, yieldSize=100000) Iteration through a BAM file requires that the file be opened, repeatedly queried inside a loop,thenclosed





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