Monica-Mweetwa/Africa-MetaAnalysis-Archive

This is the archive for code used to generate results reported in the paper titled: A META-ANALYSIS OF GUT MICROBIOME RESEARCH IN MALNOURISHED AFRICAN POPULATIONS: A NATURAL LANGAUGE PROCESSING APPROACH # Africa-MetaAnalysis-Archive This is the archive for code used to generate results reported in the paper titled: A META-ANALYSIS OF GUT MICROBIOME RESEARCH IN MALNOURISHED AFRICAN POPULATIONS: A NATURAL LANGAUGE PROCESSING APPROACH HTML files from pubmed central were donwloaded and converted to json files using AutoCorpus. The microbe names were extracted using MicrobELP. * The first step at annotation was extraction of microbes from json files which was executed in python using the code file: Extract_annotations.ipynb * The next step was summarisation of study characteristics manually extracted from text which was implemented in python using the code file: PythonAnnotation_Dec.ipynb * Phylogenetic tree creation and annotation was done in 3 ways: * A) Phylogenetic tree of all studies included in the analysis: PhyloTrees_12052025.Rmd * B) Phylogenetic tree of all studies included stratified by region and sequencing method: PhyloTrees_12052025.Rmd * C) Phylogenetic tree of all studies that compared healthy and undernourished children: CaCo_PhyPlot_12052025.R The imput data used is stored in the 'Data' folder. * The data used for phylogenetic tree constraction is stored in the 'Data/All_Studies' folder * The case control analysis used data stored in the 'Data/CaseControl_Analysis' # Contact Information If you have any questions or comments with the code, please feel free to contact: - **Lead Author**: [Monica N Mweetwa] **Email**: [monica@tropgan.com] **Institution**: [TROPGAN]