- Add get_track_df for gene track plot.
- Add metagene_plot for metagene analysis.
- Add triAmino_motif_plot for enriched motif logo plot.
- Add get_pausing_site to detect pausing site across transcipt. The method is using PausePred described with a sliding window. More details please refer to PausePred and Rfeet: webtools for inferring ribosome pauses and visualizing footprint density from ribosome profiling data
- Add 5'end or 3'end assginment of reads for pre_qc_data function.
- Add in-frame information for aggregaton plot.
- Add peptide_motif_score2 to calculate average pausec score according to The ubiquitin conjugase Rad6 mediates ribosome pausing during oxidative stress reference.
- Add show_cds_region_only parameter for track_plot.
- Add calculatePolarity2 to calculate polarity score for nomalized data.
- Add frame_col parameter for metagene_plot.
- Constructed into a ribosomeObj Object, methods can be applied on ribosomeObj Object.
- Implementary with RiboSeqTools package functions to deal with selective ribosome profilling data.
- Add ribo_bam_to_bw to transform ribo bamfiles to bigwig.
- Add XAM_version for ribo_bam_to_bw and *pre_qc_data to choose suitable XAM version to analysis.
- Add rpm and average normalization for get_nomalized_counts.
- Add periodicity_check function which applied Discrete Fourier transform method to check periodicity.
- Add single_gene_plot function to visualize single gene profile of ribosome data.
- Add codonRelativeDist.py to calculate relative codon occupancy along transcript.
- Add *bam_to_bw to convert bam files to bigwigs.
- Add get_counts_from_bam to extract counts for ribo or rna bam files.