RiboParser documentation¶
RiboParser is a modular command-line toolkit for comprehensive RNA-seq and Ribo-seq data analysis.
This documentation keeps the repository README short and moves the complete tutorial, parameter explanations, command templates, output interpretation, and helper scripts into a structured website.
Complete workflow¶
Reference preparation
→ Raw data download
→ Raw data cleaning
→ Alignment and quantification
→ Quality control
→ Gene-level analysis
→ Codon-level analysis
→ smORF analysis
→ SeRP analysis
→ Visualization and downstream analysis
Main command groups¶
| Group | Commands |
|---|---|
| Ribo-quality | rpf_Reference, rpf_Check, rpf_Digest, rpf_Offset, rpf_Density, rpf_Merge, rpf_Periodicity, rpf_Metaplot, rpf_Coverage, rpf_Corr, rpf_Quant, rpf_Percent |
| RNA | rna_Offset, rna_Density |
| Ribo-pausing | rpf_Pausing, rpf_Occupancy, rpf_CoV, rpf_Cumulative_CoV, rpf_CDT, rpf_CST, rpf_Odd_Ratio, rpf_Meta_Codon |
| Ribo-utils | rpf_Shuffle, rpf_Shift, rpf_Retrieve, rpf_Bam2bw, rpf_Geneplot |
| smORF | smorf_scanner, smorf_filter, smorf_evidence, smorf_integrate |
| SeRP | serp_overlap, serp_peak, serp_properties |
| Helper scripts | FASTA, FASTQ, bedGraph, Bowtie, merge_ribo, RiboCode, RiboTISH, RSEM, Unix helpers |
Example dataset¶
The original workflow uses GSE67387 as an example dataset.