2024
Autores
Soeiro, R; David, G; Neves, A;
Publicação
Journal on Teaching Engineering
Abstract
2024
Autores
Peres, A; Klein, V; Frankel, B; Lees, W; Polak, P; Meehan, M; Rocha, A; Lopes, JC; Yaari, G;
Publicação
BRIEFINGS IN BIOINFORMATICS
Abstract
Enhancing the reproducibility and comprehension of adaptive immune receptor repertoire sequencing (AIRR-seq) data analysis is critical for scientific progress. This study presents guidelines for reproducible AIRR-seq data analysis, and a collection of ready-to-use pipelines with comprehensive documentation. To this end, ten common pipelines were implemented using ViaFoundry, a user-friendly interface for pipeline management and automation. This is accompanied by versioned containers, documentation and archiving capabilities. The automation of pre-processing analysis steps and the ability to modify pipeline parameters according to specific research needs are emphasized. AIRR-seq data analysis is highly sensitive to varying parameters and setups; using the guidelines presented here, the ability to reproduce previously published results is demonstrated. This work promotes transparency, reproducibility, and collaboration in AIRR-seq data analysis, serving as a model for handling and documenting bioinformatics pipelines in other research domains.
2024
Autores
Bertolino, A; Pascoal Faria, J; Lago, P; Semini, L;
Publicação
Communications in Computer and Information Science
Abstract
2024
Autores
Bertolino, A; Faria, JP; Lago, P; Semini, L;
Publicação
QUATIC
Abstract
2024
Autores
Pereira, A; Lima, B; Faria, JP;
Publicação
CoRR
Abstract
2024
Autores
Faria, JP; Verbeek, F; Fasolino, AR;
Publicação
ACM SIGSOFT Softw. Eng. Notes
Abstract
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