Man pages for jeffbhasin/goldmine
goldmine: Genomic context annotation for any set of genomic ranges using UCSC Genome Browser tables
| 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 |
