| col.abs | Color scale for a specified quantile. This scale is intended... |
| col.z | Color scale for a specified quantile. This scale is intended... |
| cond.col | Color scale for categorical data. |
| cond.col.vec | Creates a color scale for the levels in a vector, then... |
| CrobustaMotifs | PWMs for 1487 potential TF binding sites. |
| dir.apply | Wrapper for applying a write function to each element of list... |
| dir.csv | Concatenates a path, filename, and file extension into an... |
| dir.eps | Concatenates a path, filename, and file extension into an... |
| dir.export | Concatenates a path, filename, and file extension into an... |
| dir.gg | Concatenates a path, filename, and file extension into an... |
| dir.hist | Accepts a numeric vector and writes a histogram in EPS format... |
| dir.img | Concatenates a path, filename, and file extension into an... |
| dir.out | Concatenates a path, filename, and file extension into an... |
| dir.pdf | Concatenates a path, filename, and file extension into an... |
| dir.png | Concatenates a path, filename, and file extension into an... |
| dir.svg | Concatenates a path, filename, and file extension into an... |
| dir.tab | Concatenates a path, filename, and file extension into an... |
| getFeatures | Parses a genome file in GFF format into a list of... |
| getMatches | Searches a given set of genomic ranges for the motifs... |
| getOverlapMat | Converts gene-peak table to a logical matrix of associations |
| getOverlaps | Finds all overlaps between one of the genomic features... |
| hm.ann | Wrapper for 'hm.cell()' which applies cell dimensions to... |
| hm.cell | Wrapper for 'Heatmap()' which allows specifying cell... |
| hmdot | accepts the results of a hypergeometric test applied to each... |
| lrtab | Applies a function to all file names in a specified directory... |
| matchPois | Accepts a vector of peak IDs, and performs a Poisson test for... |
| mkdate | Creates a file path from a name, directory, and extension,... |
| regMat | Determines a matrix of potential regulatory TFs. |
| rmdup | Accepts a PWMatrixList and an output from... |
