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It integrates many functional analysis modules, range from basic processing to downstream analysis. All the processes are embedded in Nextflow with Docker support, which ensures high reproducibility and scalability of the analysis. MeRIPseqPipe is particularly suitable for analyzing a large number of samples at once with a simple command. The final output directory is structured based on each step and tool. And visualization reports containing various tables and plots are provided as HTML files.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>MeRIPseqPipe is freely available at https:\/\/github.com\/canceromics\/MeRIPseqPipe.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac025","type":"journal-article","created":{"date-parts":[[2022,1,10]],"date-time":"2022-01-10T20:11:14Z","timestamp":1641845474000},"page":"2054-2056","source":"Crossref","is-referenced-by-count":9,"title":["MeRIPseqPipe: an integrated analysis pipeline for MeRIP-seq data based on Nextflow"],"prefix":"10.1093","volume":"38","author":[{"given":"Xiaoqiong","family":"Bao","sequence":"first","affiliation":[{"name":"State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University , Guangzhou 510060, China"}]},{"given":"Kaiyu","family":"Zhu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University , Guangzhou 510060, China"}]},{"given":"Xuefei","family":"Liu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University , Guangzhou 510060, China"}]},{"given":"Zhihang","family":"Chen","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University , Guangzhou 510060, China"}]},{"given":"Ziwei","family":"Luo","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University , Guangzhou 510060, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8683-6145","authenticated-orcid":false,"given":"Qi","family":"Zhao","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University , Guangzhou 510060, China"}]},{"given":"Jian","family":"Ren","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University , Guangzhou 510060, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2492-2689","authenticated-orcid":false,"given":"Zhixiang","family":"Zuo","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University , Guangzhou 510060, China"}]}],"member":"286","published-online":{"date-parts":[[2022,1,12]]},"reference":[{"key":"2023020109000809000_btac025-B1","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: an ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"2023020109000809000_btac025-B2","doi-asserted-by":"crossref","first-page":"i378","DOI":"10.1093\/bioinformatics\/btw281","article-title":"A novel algorithm for calling mRNA m6A peaks by modeling biological variances in MeRIP-seq data","volume":"32","author":"Cui","year":"2016","journal-title":"Bioinformatics"},{"key":"2023020109000809000_btac025-B3","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1038\/nbt.3820","article-title":"Nextflow enables reproducible computational workflows","volume":"35","author":"Di Tommaso","year":"2017","journal-title":"Nat. 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