{"title":"CRAK-Velo：染色质可及性动力学集成改进了 RNA 速度估算","authors":"Nour El Kazwini, Mingze Gao, Idris Kouadri Boudjelthia, Fangxin Cai, Yuanhua Huang, Guido Sanguinetti","doi":"10.1101/2024.09.12.612736","DOIUrl":null,"url":null,"abstract":"RNA velocity has recently emerged as a key tool in the analysis of single-cell transcriptomic data, yet connecting RNA velocity analyses to underlying regulatory processes has proved challenging. Here we propose CRAK-Velo, a semi-mechanistic model which integrates chromatin accessibility data in the estimation of RNA velocities. CRAK-Velo provides biologically consistent estimates of developmental flows and enables accurate cell-type deconvolution, while additionally shining light on regulatory processes at the level of interactions between genes and chromatin regions.","PeriodicalId":501307,"journal":{"name":"bioRxiv - Bioinformatics","volume":"65 1","pages":""},"PeriodicalIF":0.0000,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"CRAK-Velo: Chromatin Accessibility Kinetics integration improves RNA Velocity estimation\",\"authors\":\"Nour El Kazwini, Mingze Gao, Idris Kouadri Boudjelthia, Fangxin Cai, Yuanhua Huang, Guido Sanguinetti\",\"doi\":\"10.1101/2024.09.12.612736\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"RNA velocity has recently emerged as a key tool in the analysis of single-cell transcriptomic data, yet connecting RNA velocity analyses to underlying regulatory processes has proved challenging. Here we propose CRAK-Velo, a semi-mechanistic model which integrates chromatin accessibility data in the estimation of RNA velocities. CRAK-Velo provides biologically consistent estimates of developmental flows and enables accurate cell-type deconvolution, while additionally shining light on regulatory processes at the level of interactions between genes and chromatin regions.\",\"PeriodicalId\":501307,\"journal\":{\"name\":\"bioRxiv - Bioinformatics\",\"volume\":\"65 1\",\"pages\":\"\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2024-09-17\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"bioRxiv - Bioinformatics\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1101/2024.09.12.612736\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"bioRxiv - Bioinformatics","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1101/2024.09.12.612736","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
RNA velocity has recently emerged as a key tool in the analysis of single-cell transcriptomic data, yet connecting RNA velocity analyses to underlying regulatory processes has proved challenging. Here we propose CRAK-Velo, a semi-mechanistic model which integrates chromatin accessibility data in the estimation of RNA velocities. CRAK-Velo provides biologically consistent estimates of developmental flows and enables accurate cell-type deconvolution, while additionally shining light on regulatory processes at the level of interactions between genes and chromatin regions.
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