addGenes | Add columns with distance to nearest gene and gene symbol(s) |
addNearest | Add columns to query with distance to nearest subject and... |
drawGenomePool | Draw a length-matched pool of sequences from the genome |
getCpgFeatures | Generate feature sets based on CpG island, shore, and shelf... |
getFeatures | Obtain feature sets from UCSC genome browser tables |
getGeneModels | Return sets of ranges for individual gene model components... |
getGenes | Load table of gene ranges via UCSC Genome Browser tables |
getUCSCTable | Load an annotation table from the UCSC Genome Browser as an R... |
ggnice | Nice ggplot2 theme |
gmWrite | Write individual CSV files to disk from the output of... |
goldmine | Explore relationships between a set of genomic ranges and... |
goldmine-package | goldmine: Genomic context annotation for any set of genomic... |
makeDT | Make a data.table from a GRanges or a data.frame |
makeGRanges | Make a GRanges from a data.frame or data.table with the... |
readUCSCAnnotation | Read UCSC table files from disk and join all related tables |
sortDT | Sort a data.frame, data.table, or GRanges by chr (accounting... |
sortGRanges | Sort a data.frame, data.table, or GRanges by chr (accounting... |
writeBEDFromGRanges | Write a BED format file from a GenomicRanges object |
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