{"doi":"10.1093/bioinformatics/btac093","title":"riboviz 2: a flexible and robust ribosome profiling data analysis and visualization workflow","abstract":"MOTIVATION: Ribosome profiling, or Ribo-seq, is the state-of-the-art method for quantifying protein synthesis in living cells. Computational analysis of Ribo-seq data remains challenging due to the complexity of the procedure, as well as variations introduced for specific organisms or specialized analyses. RESULTS: We present riboviz 2, an updated riboviz package, for the comprehensive transcript-centric analysis and visualization of Ribo-seq data. riboviz 2 includes an analysis workflow built on the Nextflow workflow management system for end-to-end processing of Ribo-seq data. riboviz 2 has been extensively tested on diverse species and library preparation strategies, including multiplexed samples. riboviz 2 is flexible and uses open, documented file formats, allowing users to integrate new analyses with the pipeline. AVAILABILITY AND IMPLEMENTATION: riboviz 2 is freely available at github.com/riboviz/riboviz.","journal":"Bioinformatics","year":2022,"id":273658,"datarank":0.5517790374013725,"base_score":2.3978952727983707,"endowment":2.3978952727983707,"self_citation_contribution":0.3596842909197557,"citation_network_contribution":0.19209474648161678,"self_endowment_contribution":0.3596842909197557,"citer_contribution":0.19209474648161678,"corpus_percentile":null,"corpus_rank":null,"citation_count":10,"citer_count":8,"citers_with_citation_signal":7,"citers_with_endowment":7,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.8519,"is_data_producer":true,"deposit_databanks":{"figshare":["10.6084/m9.figshare.12624200"]},"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":820463,"name":"Felicity Anderson","orcid":"0000-0001-8778-6779","position":1,"is_corresponding":false},{"id":819216,"name":"John Favate","orcid":"0000-0001-6344-4854","position":2,"is_corresponding":false},{"id":820464,"name":"Michael Jackson","orcid":"0000-0002-1765-8234","position":3,"is_corresponding":false},{"id":554244,"name":"Amanda Mok","orcid":"0000-0001-6981-1547","position":4,"is_corresponding":false},{"id":820465,"name":"Anna Kurowska","orcid":"0000-0003-1261-7377","position":5,"is_corresponding":false},{"id":941166,"name":"Junchen Liu","orcid":"0000-0003-4740-3395","position":6,"is_corresponding":false},{"id":820466,"name":"Emma MacKenzie","orcid":"0000-0003-0096-200X","position":7,"is_corresponding":false},{"id":588170,"name":"Vikram S. Shivakumar","orcid":"0000-0002-1424-3711","position":8,"is_corresponding":false},{"id":646705,"name":"Peter Tilton","orcid":"0000-0003-1238-6468","position":9,"is_corresponding":false},{"id":820467,"name":"Sophie Winterbourne","orcid":"0000-0001-9109-285X","position":10,"is_corresponding":false},{"id":820468,"name":"Siyin Xue","orcid":"0000-0001-8101-564X","position":11,"is_corresponding":false},{"id":820469,"name":"Kostas Kavoussanakis","orcid":"0000-0001-9167-7145","position":12,"is_corresponding":false},{"id":554246,"name":"Liana F. Lareau","orcid":"0000-0003-3223-3426","position":13,"is_corresponding":false},{"id":17872,"name":"Premal Shah","orcid":"0000-0002-8424-4218","position":14,"is_corresponding":false},{"id":17889,"name":"Edward W. J. Wallace","orcid":"0000-0001-8025-6361","position":15,"is_corresponding":false},{"id":755931,"name":"Alexander L. Cope","orcid":"0000-0002-5756-7812","position":0,"is_corresponding":true}],"reference_count":19,"raw_metadata":null,"created_at":"2026-07-19T00:28:03.504676Z","pmid":"35157051","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}