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| cogstab | A data frame of COGS categories |
| colors.byexpression | Create a vector of "red" and "green" colors (or greyscale) for use by plotrange |
| find.region | Find regions of interest in prokaryotic genomes |
| IFR | Microarray data from Eriksson et al (2003) |
| linkem.avg | Link togther two data frames, one representing the genome, the other representing numerical data |
| PGE.barplot | Slightly customised version of barplot |
| PGE.prepare | Internal function of ProGenExpress |
| plot.cogs.legend | Plot a legend of the COGS categories |
| plotrange | Plot numerical values on a genome, setting the range by base number |
| plotrange.bygene | Plot numerical values on a genome, setting the range by gene name |
| plotrange.vertical | Plot numerical values on a genome, setting the range by base number |
| read.GenBank | Attempt to read an NCBI RefSeq entry into a data frame |
| read.NCBI | Attempt to download and read .ptt files from the NCBI |
| read.ptt | Read an NCBI .ptt file |
| show.region | A utility function from ProGenExpress which prints the data for a genomic region to the screen and draws a plot of that region |
| STLT2 | Data frame describing the Salmonella typhimurium genome |