{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,18]],"date-time":"2026-06-18T07:12:36Z","timestamp":1781766756542,"version":"3.54.5"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T00:00:00Z","timestamp":1774310400000},"content-version":"vor","delay-in-days":82,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82303953"],"award-info":[{"award-number":["82303953"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004735","name":"Hunan Provincial Natural Science Foundation of China","doi-asserted-by":"crossref","award":["2025JJ40079"],"award-info":[{"award-number":["2025JJ40079"]}],"id":[{"id":"10.13039\/501100004735","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Central South University Startup Funding"},{"name":"Noncommunicable Chronic Diseases-National Science and Technology Major Project","award":["2023ZD0502105"],"award-info":[{"award-number":["2023ZD0502105"]}]},{"name":"Ministry of Education in China Liberal arts and Social Sciences Foundation","award":["24YJCZH462"],"award-info":[{"award-number":["24YJCZH462"]}]},{"name":"Youth Science and Technology Elite Talent Project of Guizhou Provincial Department of Education","award":["QJJ-2024-333"],"award-info":[{"award-number":["QJJ-2024-333"]}]},{"name":"Excellent Young Talent Cultivation Project of Zunyi City","award":["142"],"award-info":[{"award-number":["142"]}]},{"name":"Future Science and Technology Elite Talent Cultivation Project of Zunyi Medical University"},{"name":"Key Program of the Education Sciences Planning of Guizhou Province"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Modern computational biology relies heavily on command-line tools that underpin analytical workflows, yet integrating these tools into R-based analyses poses substantial challenges for reproducibility, especially for researchers with limited computational expertise. While R excels at statistical analysis and visualization, its native capabilities for executing external commands remain rudimentary, lacking structured integration, environment management, and reliable cross-platform support.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>To address these limitations, BLIT, an R package, provides a unified framework for seamless command-line integration within R, enabling R users to invoke external tools in an intuitive manner. Rather than positioning itself as yet another workflow manager, BLIT emphasizes the robust encapsulation and coordination of command-line tools, enabling users to construct reproducible analysis pipelines without leaving the R environment. BLIT encapsulates command-line programs as R6 objects with dynamic validation, Micromamba-based environment management, and native piping support. This makes BLIT a direct bridge between R scripts and heterogeneous command-line ecosystems, replacing fragile system() calls with a robust, standardized framework that supports conditional execution and single-machine parallel computing, with the capability to hand off constructed command workflows to HPC schedulers or workflow engines for large-scale execution. Although designed for bioinformatics, BLIT offers a general, platform-agnostic solution for constructing reproducible analytical pipelines within R.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>BLIT is available on CRAN (https:\/\/cran.r-project.org\/package=blit) and on GitHub (https:\/\/github.com\/WangLabCSU\/blit).<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioadv\/vbag088","type":"journal-article","created":{"date-parts":[[2026,3,21]],"date-time":"2026-03-21T12:36:29Z","timestamp":1774096589000},"source":"Crossref","is-referenced-by-count":1,"title":["BLIT: an R package for seamless integration of command-line bioinformatics tool universe"],"prefix":"10.1093","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0009-0002-2530-0897","authenticated-orcid":false,"given":"Jia","family":"Ding","sequence":"first","affiliation":[{"name":"Department of Biomedical Informatics, School of Life Sciences, Central South University , Changsha, 410013, P. 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