{"categories":[{"label":"Information Analysis","url":"https://skillfed.io/packages/category/scientific-engineering-information-analysis/2"}],"enrichment":{"capability":"RUST normalizes ribosome profiling (Ribo-seq) data to reduce noise and heterogeneity, enabling analysis of how mRNA sequence features affect ribosome footprint densities.","skillfed_tags":["bioinformatics","ribo-seq","abandoned"],"use_cases":["Normalize Ribo-seq datasets before analyzing how codon usage or secondary structure affects ribosome occupancy","Perform quality control on ribosome profiling experiments to identify protocol-related artifacts before downstream analysis","Extract normalized ribosome footprint parameters for predictive modeling of local ribosome densities","Compare ribosome decoding rates across different mRNA regions after removing heterogeneous noise"],"what_it_does":"RUST is a normalization method for ribosome profiling (Ribo-seq) data that addresses the characteristic problem of high-density peaks and alignment gaps in ribosome footprint measurements. It implements a unit step transformation designed to reduce the impact of data heterogeneity and noise, making it easier to identify which mRNA sequence features correlate with ribosome footprint densities.\n\nThe package depends on pysam for sequence alignment handling, matplotlib for visualization, and numpy for numerical computation. It targets Python 3.8 and later. The tool was developed as part of published research demonstrating that RUST outperforms other normalization techniques and can extract parameters sufficient for predicting experimental densities with high accuracy.","worth_installing":"No. The project is abandoned (last commit March 2023, over 1200 days ago) with no maintenance signal and zero repository stars. While the MIT license is permissive and installation friction is low, the lack of active maintenance means bugs, security issues, or compatibility problems with current dependency versions will not be fixed. For active Ribo-seq analysis work, seek a maintained alternative or fork."},"id":"rust","links":{"html":"https://skillfed.io/packages/rust","md":"https://skillfed.io/packages/rust.md","pypi":"https://pypi.org/project/rust/"},"maintenance":{"status":"abandoned"},"meta":{"latest_release":"2023-05-02","license_spdx":null,"license_treatment":"permissive","name":"RUST","python_support":"supports_current","summary":"Unit step transformation of Ribo-Seq data"},"popularity":{"monthly_downloads":276812,"position":8157,"tier":"top_15000"},"security":{"n_vulnerabilities":0},"version":"1.3.1"}