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. |
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" |