{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T16:53:34Z","timestamp":1785430414560,"version":"3.56.0"},"posted":{"date-parts":[[2025,5,10]]},"group-title":"Bioinformatics","reference-count":19,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,5,10]],"date-time":"2025-05-10T00:00:00Z","timestamp":1746835200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"award":["R35GN118103"],"award-info":[{"award-number":["R35GN118103"]}],"id":[{"id":"https:\/\/ror.org\/04q48ey07","id-type":"ROR","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000928","name":"Welch Foundation","doi-asserted-by":"crossref","award":["I-2184"],"award-info":[{"award-number":["I-2184"]}],"id":[{"id":"10.13039\/100000928","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,5,10]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Reproducibility and accessibility are cardinal principles in the rapidly evolving field of bioinformatics. As the collection of biological data grows, proper use of pipelines to analyze datasets can become a bottleneck restricting efficient analysis. Biologists who collect data and test hypotheses may not have strong computational backgrounds and may not be able to fully understand the underlying strengths and weaknesses of computational approaches or fully exploit their data. Some data may be misunderstood and, perhaps more importantly, critical findings may remain unobserved. High throughput RNA sequencing (RNAseq) has advanced our understanding of transcriptomics across diverse applications. Here we introduce g.nome, a bioinformatics platform that integrates contemporary tools necessary for independent analysis. A user-friendly graphical interface simplifies running jobs and allows simplified analysis of different datasets by non-bioinformaticians. g.nome was used to analyze the consequences of localizing the critical RNAi factor argonaute (AGO) to nuclei of colorectal cancer cell line HCT116. Analysis using the pipeline facilitated the straightforward identification of splicing changes and the prioritization of these splicing changes for validation and further experimental analysis.\n                  <jats:fig id=\"ufig1\" position=\"float\" orientation=\"portrait\" fig-type=\"figure\">\n                    <jats:graphic xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"652286v1_ufig1\" position=\"float\" orientation=\"portrait\"\/>\n                  <\/jats:fig>\n                <\/jats:p>","DOI":"10.1101\/2025.05.09.652286","type":"posted-content","created":{"date-parts":[[2025,5,10]],"date-time":"2025-05-10T23:20:13Z","timestamp":1746919213000},"source":"Crossref","is-referenced-by-count":0,"title":["g.nome, A Transparent Bioinformatics Pipeline that Enables Differential Expression and Alternative Splicing Analysis by Non-Computational Biologists"],"prefix":"10.64898","author":[{"given":"Rut","family":"Bryl","sequence":"first","affiliation":[{"name":"UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75390-9041"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Krystal C.","family":"Johnson","sequence":"additional","affiliation":[{"name":"UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75390-9041"},{"name":"current address, Alnylam Pharmaceuticals, 675 West Kendall St., Cambridge, MA 02142"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiongbin","family":"Kang","sequence":"additional","affiliation":[{"name":"Quantitative Biomedical Research Center, Peter O\u2019Donnell Jr. School of Public Health, UT Southwestern Medical Center Dallas, TX 75235"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tao","family":"Wang","sequence":"additional","affiliation":[{"name":"Quantitative Biomedical Research Center, Peter O\u2019Donnell Jr. School of Public Health, UT Southwestern Medical Center Dallas, TX 75235"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kit A.","family":"Fuhrman","sequence":"additional","affiliation":[{"name":"Almaden Genomics, 1409 Botham Jean Blvd, Suite 1007, Dallas, TX 75215"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark","family":"Kunitomi","sequence":"additional","affiliation":[{"name":"Almaden Genomics, 1409 Botham Jean Blvd, Suite 1007, Dallas, TX 75215"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nora","family":"Kearns","sequence":"additional","affiliation":[{"name":"Almaden Genomics, 1409 Botham Jean Blvd, Suite 1007, Dallas, TX 75215"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David R.","family":"Corey","sequence":"additional","affiliation":[{"name":"UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75390-9041"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026041121211043000_2025.05.09.652286v1.1","doi-asserted-by":"publisher","DOI":"10.1038\/nrg2484"},{"key":"2026041121211043000_2025.05.09.652286v1.2","doi-asserted-by":"publisher","DOI":"10.1038\/nrm1857"},{"key":"2026041121211043000_2025.05.09.652286v1.3","doi-asserted-by":"crossref","unstructured":"Gruening, B ., Sallou, O., Moreno, P., da Veiga Leprevost, F., Menager, H., Sondergaard, D., Rost, H., Sachsenberg, T., O\u2019Connor, B., Madeira, F., et al. (2018) Recommendations for the packaging and containerizing of bioinformatics software. 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(2021) Argonaute Binding within Human Nuclear RNA and its Impact on Alternative Splicing. 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