Data analysis pipeline for investigating drug-host-microbiome relationships in cardiometabolic disease (MetaCardis cohort).
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*******************************************************************<br> MetaDrugs workflow<br> ******************************************************************* Data analysis pipeline for investigating drug-host-microbiome relationships in cardiometabolic disease (MetaCardis cohort). For questions and requests, please contact:<br> Sofia K. Forslund (sofia.forslund@mdc-berlin.de)<br> and Till Birkner (till.birkner@mdc-berlin.de) *******************************************************************<br> Contents:<br> -------------------------------------------------------------------<br> Data files:<br> metadata.tar.gz - archived cohort metadata files<br> input_features.tar.gz - archived preprocessed serum and urine metabolome and gut microbiome features<br> output_complete.tar.gz - archived example analysis output files for each of the input feature file<br> output_rerun.tar.gz - archived empty directory for generating test output files as described in this document<br> -------------------------------------------------------------------<br> Text files:<br> archived in feature_names.tar.gz:<br> atcs_names - full names for atcs drug compounds<br> contrast_names - full names for disease comparison groups<br> file_names - brief description of the files in input_features folder<br> gmm_names - full names of GMM modules<br> kegg_names - full names of KEGG modules<br> ko_names - full names of KO modules<br> metadata_names - full names of metadata features<br> mOTU_names - species names for metagenomics data<br> taxon_names - taxon names for metagenomics data<br> -------------------------------------------------------------------<br> Scripts:<br> -------------------------------------------------------------------<br> runFrame.r - main wrapper script envoking the analysis pipeline<br> -------------------------------------------------------------------<br> runFrame_rel_comb.r - script calculating drug combination effects<br> runFrame_rel.r - script calculating dosage effects<br> testCombPresenceSeparate.r - testing of significant drug combination effects beyond single drug effects<br> testDosagePresenceSeparate.pl - testing of significant drug dosage effects beyond single drug effects<br> testDosagePresenceSeparateNegative.pl - testing of unique drug dosage effects beyond single drug effects<br> -------------------------------------------------------------------<br> prettifyResults_uncollapsed.pl - wrapper scripts to create and format a single analysis output file<br> makeTables.r - wrapper script to make excel tables with analysis results<br> -------------------------------------------------------------------<br> Example output file:<br> -------------------------------------------------------------------<br> output_all_formatted_noc_uncollapsed_complete.tsv - contains all disease-drug-host-microbiome feature analysis results in one place.<br> *******************************************************************
******************************************************************* MetaDrugs 分析流程 ******************************************************************* 用于探究心血管代谢疾病中药物-宿主-微生物组关联的数据分析管线（基于MetaCardis队列）。如有疑问与需求，请联系： 索菲亚·K·福斯隆德（sofia.forslund@mdc-berlin.de） 以及蒂尔·伯克纳（till.birkner@mdc-berlin.de） ******************************************************************* 内容一览： ------------------------------------------------------------------- 数据文件： metadata.tar.gz - 归档的队列元数据文件 input_features.tar.gz - 归档的预处理血清、尿液代谢组与肠道微生物组特征文件 output_complete.tar.gz - 归档的各输入特征文件对应的示例分析结果文件 output_rerun.tar.gz - 归档空目录，用于按本文档说明生成测试输出文件 ------------------------------------------------------------------- 文本文件： 归档于feature_names.tar.gz中： atcs_names - ATC (Anatomical Therapeutic Chemical)药物化合物完整名称 contrast_names - 疾病对比组完整名称 file_names - input_features文件夹内各文件的简要说明 gmm_names - GMM (Gaussian Mixture Model)模块完整名称 kegg_names - KEGG (Kyoto Encyclopedia of Genes and Genomes)模块完整名称 ko_names - KO (KEGG Orthology)模块完整名称 metadata_names - 元数据特征完整名称 mOTU_names - 宏基因组学数据的物种名称 taxon_names - 宏基因组学数据的分类单元名称 ------------------------------------------------------------------- 脚本： ------------------------------------------------------------------- runFrame.r - 调用分析管线的主包装脚本 ------------------------------------------------------------------- runFrame_rel_comb.r - 计算药物联合效应的脚本 runFrame_rel.r - 计算药物剂量效应的脚本 testCombPresenceSeparate.r - 检测超越单一药物效应的显著药物联合效应的脚本 testDosagePresenceSeparate.pl - 检测超越单一药物效应的显著药物剂量效应的脚本 testDosagePresenceSeparateNegative.pl - 检测超越单一药物效应的独特药物剂量效应的脚本 ------------------------------------------------------------------- prettifyResults_uncollapsed.pl - 用于创建并格式化单份未合并分析结果文件的包装脚本 makeTables.r - 用于生成含分析结果的Excel表格的包装脚本 ------------------------------------------------------------------- 示例输出文件： ------------------------------------------------------------------- output_all_formatted_noc_uncollapsed_complete.tsv - 整合了所有疾病-药物-宿主-微生物组特征分析结果的单文件。 *******************************************************************
