| riboSeqR-package | Analysis of sequencing data from ribosome profiling experiments. |
| filterHits | Filters framecalled data based on the mean number of hits observed across a replicate group. |
| findCDS | Parses a transcriptome file looking for start/stop codons in frame. |
| frameCounting | Counts aligned reads within coding sequence regions by frame and footprint size, splitting by frame and footprint size. |
| lengthDist | A function plotting the density of lengths in a riboData object. |
| libScales | Generates library scaling factors from ribosome footprint (and associated RNA) data. |
| logoContext | Produces a motif of coding start context |
| plotCDS | Plots average ribosome footprint alignment to coding sequences at 5' and 3' ends. |
| plotFS | Analyses frame called ribosome footprint data within coding sequences and identifies likely frame-shift of different length ribosome footprint reads. |
| plotTranscript | Plots ribosome footprint abundance and mRNA coverage (if available) for a specific transcript. |
| readingFrame | Analyses frame called ribosome footprint data within coding sequences and identifies likely frame-shift of different length ribosome footprint reads. |
| readRibodata | Reads ribosomal and (optionally) rna data from alignment files. |
| riboCoding | Class "riboCoding" |
| riboCoding-class | Class "riboCoding" |
| riboData | Class "riboData" |
| riboData-class | Class "riboData" |
| riboSeqR | Analysis of sequencing data from ribosome profiling experiments. |
| rnaCounts | Extracts mRNA counts from a riboDat object for a set of coding sequence coordinates. |
| show-method | Class "riboCoding" |
| sliceCounts | Slices out count data from riboCoding object for use in differential translation analyses. |
| [-method | Class "riboCoding" |