LIRA — Literature Integration, Ranking & Analysis

Bilingual (PT/EN) Shiny application for multi-database bibliometric analysis, article prioritization, and reading queue generation.

Description

A fully interactive R/Shiny pipeline for systematic and scoping reviews with a complete bilingual interface (Portuguese ↔ English, switchable at runtime). Supports PubMed, Web of Science, Scopus, and custom databases. Performs automatic deduplication, composite relevance scoring (thematic + bibliometric components), network analysis (keyword co-occurrence, author and country collaboration), and structured Excel export with PRISMA flow data.

Developed in the context of multi-omics research at the Núcleo de Genética Humana e Molecular (NGHM), Universidade Federal do Espírito Santo (UFES).

Features

• Bilingual interface — full PT/EN UI with instant switching, persistent across sessions
• Import from PubMed (.txt/.nbib), Web of Science (.txt), Scopus (.bib/.ris/.csv), and custom sources
• Automatic deduplication via the bibliometrix package
• Composite scoring: thematic component (field-weighted keyword match on title, keywords, abstract) + bibliometric component (citations, recency, journal tier, document type)
• Priority classification: P1 (mandatory), P2 (recommended), P3 (optional), P4 (removed)
• Structured 6-week reading queue
• Bibliometric networks with Louvain clustering (igraph); reproducible seed exposed in UI
• Recency scoring relative to search date (not hardcoded years)
• Cross-system file navigation: automatic detection of all available drives
• Export: styled multi-sheet .xlsx with PRISMA flow, annotation template, network metrics, and auto-generated methods text in PT and EN
• Figure download (PNG 300 DPI)
• Editorial-grade UI: Fraunces (display) + Plus Jakarta Sans (UI) + JetBrains Mono (numbers)

Requirements

• R ≥ 4.2
• Packages: shiny, shinydashboard, shinyFiles, shinyWidgets, bibliometrix, tidyverse, openxlsx, ggplot2, DT, waiter, igraph

install.packages(c(
  "shiny", "shinydashboard", "shinyFiles", "shinyWidgets",
  "bibliometrix", "tidyverse", "openxlsx", "ggplot2",
  "DT", "waiter", "igraph"
))

Usage

shiny::runApp("lira.R")

Citation

If you use this software in a publication, please cite:

Basílio, L.A., Casotti, M.C., Meira, D.D., Louro, I.D. (2026). LIRA: Literature Integration, Ranking & Analysis (v1.0.0). Universidade Federal do Espírito Santo (UFES), Vitória, ES, Brasil. https://doi.org/10.5281/zenodo.20454162

Authors

Leandro Araújo Basílio (author, maintainer)
Mestrando em Biotecnologia — UFES
Núcleo de Genética Humana e Molecular (NGHM)
Vitória, ES, Brasil

Matheus Correia Casotti (author — conceptualization, testing, validation)
NGHM — Universidade Federal do Espírito Santo
Vitória, ES, Brasil

Débora Dummer Meira (author, thesis advisor)
Professora — Departamento de Ciências Biológicas, UFES
Núcleo de Genética Humana e Molecular (NGHM)
Vitória, ES, Brasil

Iuri Drumond Louro (author)
NGHM — Universidade Federal do Espírito Santo
Vitória, ES, Brasil

Collaborator

Roquemar de Lima Baldam (contributor)
Universidade Federal do Espírito Santo
Vitória, ES, Brasil

License

Copyright © 2026 Basílio LA, Casotti MC, Meira DD, Louro ID. All rights reserved.
See LICENSE for details.