{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/clear-coverage-based-limiting-cell-experiment","title":"CLEAR: Coverage-based Limiting-cell Experiment Analysis for RNA-seq","arxiv_id":"1806.03142","date":"2019-05-23","proceeding":null,"authors":[],"abstract":"Direct cDNA preamplification protocols developed for single-cell RNA-seq have\nenabled transcriptome profiling of precious clinical samples and rare cells\nwithout sample pooling or RNA extraction. Currently, there is no algorithm\noptimized to reveal and remove noisy transcripts in limiting-cell RNA-seq\n(lcRNA-seq) data for downstream analyses. Herein, we present CLEAR, a workflow\nthat identifies reliably quantifiable transcripts in lcRNA-seq data for\ndifferentially expressed gene (DEG) analysis. Libraries at three input amounts\nof FACS-derived CD5+ and CD5- cells from a chronic lymphocytic leukemia patient\nwere used to develop CLEAR. When using CLEAR transcripts vs. using all\ntranscripts, downstream analyses revealed more shared transcripts across\ndifferent input RNA amounts, improved Principal Component Analysis (PCA)\nseparation, and yielded more DEGs between cell types. As proof-of-principle,\nCLEAR was applied to an in-house lcRNA-seq dataset and two public datasets.\nWhen imputation is used, CLEAR is also adaptable to large clinical studies and\nfor single cell analyses.","url_abs":"http://arxiv.org/abs/1806.03142v2","url_pdf":"http://arxiv.org/pdf/1806.03142v2.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"clear-coverage-based-limiting-cell-experiment","repo_url":"https://github.com/rbundschuh/CLEAR","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[{"task_slug":"imputation","task_name":"Imputation"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}