Man pages for jianhong/ribosomeProfilingQC
Ribosome Profiling Quality Control
| assignReadingFrame | Assign reading frame |
| codonBias | Codon usage bias |
| codonUsage | Start or Stop codon usage |
| countReads | Extract counts for RPFs and RNAs |
| coverageDepth | Extract coverage depth for gene level or transcript level |
| coverageRates | Calculate coverage rate |
| cvgd-class | Class '"cvgd"' |
| estimatePsite | Estimate P site position |
| filterCDS | Filter CDS by size |
| FLOSS | Fragment Length Organization Similarity Score (FLOSS) |
| frameCounts | Extract counts for gene level or transcript level |
| getFPKM | Get FPKM values for counts |
| getORFscore | Calculate ORFscore |
| getPsiteCoordinates | Get P site coordinates |
| ggBar | barplot by ggplot2 |
| metaPlot | Metagene analysis plot |
| normalizeTEbyLoess | Normalize the TE by Loess |
| normBy | Normalization by edgeR, DESeq2 or RUVSeq |
| normByRUVs | Normalization by RUVSeq |
| PAmotif | Metaplot of P site distribution |
| plotDistance2Codon | Metaplot of P site distribution |
| plotFrameDensity | Plot density for each reading frame |
| plotSpliceEvent | Plot splice event |
| plotTE | Plot translational efficiency |
| plotTranscript | Plot reads P site abundance for a specific transcript |
| prepareCDS | Prepare CDS |
| readsDistribution | Plot reads distribution in genomic elements |
| readsEndPlot | Plot start/stop windows |
| readsLenToKeep | Get reads length to keep by cutoff percentage |
| ribosomeReleaseScore | Ribosome Release Score (RRS) |
| shiftReadsByFrame | Shift reads by reading frame |
| simulateRPF | Simulation function |
| spliceEvent | Get splicing events |
| strandPlot | Plot the distribution of reads in sense and antisense strand |
| summaryReadsLength | Summary the reads lengths |
| translationalEfficiency | Translational Efficiency |
