RiboParser
RiboParser is a modular command-line toolkit for comprehensive RNA-seq and Ribo-seq data analysis.
📖 Documentation | 🐞 Issues | 📚 Citation | 📝 License
Overview
RiboParser provides an integrated workflow for RNA-seq and ribosome profiling (Ribo-seq) analysis, including reference preparation, raw data preprocessing, alignment, quantification, quality control, RPF density construction, gene-level analysis, codon-level analysis, SeRP analysis, smORF analysis, and downstream visualization with RiboShiny.
The full documentation is available at:
https://renscq.github.io/RiboParser/
Installation
Install the dependency packages with micromamba.
micromamba install cutadapt bowtie samtools star bedtools subread rsem gffread sra-tools \
ucsc-genepredtogtf ucsc-gtftogenepred ucsc-gff3togenepred ucsc-bedgraphtobigwig ucsc-bedsort \
-c bioconda
micromamba install pigz -c conda-forge
Install the RiboParser.
micromamba install riboparser -c rensc
# or
pip install riboparser
Quick test
riboparser -v
riboparser -c
riboparser -d
riboparser -m
Citation
Ren, S., Li, Y. & Zhou, Z.
RiboParser/RiboShiny: An integrated platform for comprehensive analysis and visualization of ribo-seq data.
Journal of Genetics and Genomics (2025).
DOI: 10.1016/j.jgg.2025.04.010
License
GPL-3.0-or-later.
1 maintainer
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