Kin selection explains the evolution of cooperation in the gut microbiota, by Simonet & McNally, 2020, Dataset S1 and codes for statistical analysis and figures production
收藏资源简介：
Dataset S1 contains all raw and processed material referred to in the published article "Kin selection explains the evolution of cooperation in the gut microbiota". R codes files provide all codes to replicate the analysis. Please refer to the README file for a description of all code files. The manifest files are those obtained by accessing the HMP portal on April 2020 under Project > HMP, Body Site > feces, Studies>WGS-PP1, File Type > WGS raw sequences set, File format > FASTQ. We also provide access to these data and codes at our GitHub (https://github.com/CamilleAnna/HamiltonRuleMicrobiome gitRepos.git) which can be cloned to directly re-run this analysis. <strong>Legends for Dataset S1:</strong> Sheet 1: Metagenomic samples used and access links. Sheet 2: Reference on bacterial cooperation retrieved from Web of Science search: TI¯((microb* OR bacter* OR microorganis* OR micro-organis*) AND (coop* OR social*) Sheet 3: Retained bacteria cooperation keywords Sheet 4: GOs identified by annotating all MIDAS database genomes (5944 genomes) with PANNZER2. Sheet 5: Full list of potential bacterial cooperation GO terms and description of manual curation decisions. Sheet 6: Final list of bacterial cooperation GO used for the analysis Sheet 7: Genomic diversity of the bacterial population within and across host. Computed from MIDAS snp_diversity.py pipeline. Sheet 8: final dataset for statistical analysis. Sheet 9: per-gene annotation of cooperation.
数据集S1包含已发表论文《亲缘选择解释肠道菌群合作的演化》中提及的所有原始与处理后材料。配套的R代码文件包含复现所有分析所需的全部代码，所有代码文件的详细说明请参阅README文件。 清单文件（manifest files）为2020年4月通过人类微生物组计划（Human Microbiome Project, HMP）门户网站获取的文件，具体筛选条件为：项目> HMP、身体部位>粪便、研究>WGS-PP1、文件类型>全基因组测序原始序列集、文件格式>FASTQ。本研究同时在GitHub仓库（https://github.com/CamilleAnna/HamiltonRuleMicrobiome gitRepos.git）公开了上述数据与代码，克隆该仓库即可直接复现本研究的分析流程。 <strong>数据集S1各工作表说明：</strong> 工作表1：所用宏基因组样本及获取链接 工作表2：通过Web of Science数据库检索获取的细菌合作相关参考文献，检索式为：TI=((microb* OR bacter* OR microorganism* OR micro-organism*) AND (coop* OR social*)) 工作表3：筛选保留的细菌合作相关关键词 工作表4：通过PANNZER2工具对MIDAS数据库中全部基因组（共5944个）进行注释后得到的基因本体（Gene Ontology, GO）条目 工作表5：潜在细菌合作相关GO条目的完整清单，以及手动审定规则的详细说明 工作表6：本分析所用的细菌合作相关GO条目最终列表 工作表7：宿主内部与跨宿主的细菌种群基因组多样性数据，通过MIDAS的snp_diversity.py流程计算得到 工作表8：用于统计分析的最终数据集 工作表9：各基因的合作功能注释
