Introduction | Key differences between DNAcycP2 and DNAcycP | Available formats of DNAcycP2 and DNAcycP | Installation | Usage | Main Functions | Selecting the Prediction Model | Parallelization with cycle_fasta | Example 1: fasta file input | Example 2: input as a list/vector of sequences | DNAcycP2 prediction -- Normalized vs unnormalized | Save DNAcycP2 prediciton to external file | Example 3 (Single Sequence): | Example 4: DNAStringSet object input | References | Session info

NuPoP versions hightlights | About NuPoP | NuPoP functions | Session info

What is DegNorm? | DegNorm pipline available formats | DegNorm version 1.3.4 updates | Install DegNorm R package | DegNorm main features | 1. Compute coverage score based on alignment .bam files | Set up input file: .bam and .gtf files. | Run main function to create read coverage matrix and read counts | 2. DegNorm core algorithm | 3. Plot functions in DegNorm | -- Plot the before-/after-degradation coverage curves | -- Boxplot of the degradation index(DI) scores | -- Heatmap plot of the degradation index(DI) scores | -- Correlation matrix plot of degradation index(DI) scores | Session info

Maintainer: Ji-Ping Wang, <[email protected]> | What is RiboDiPA? | RiboDiPA pipeline | Installation | Input files | RiboDiPA main features | The RiboDiPA pipeline | 0. Ribo-DiPA Wrapper Function | 1. P-site mapping | 2. Data binning | 3. Differential pattern analysis | 4. Plotting and genome visualization | Individual gene plotting | Track plotting via genome browser | Conclusion | Session info