{ "_id": "6a102bbcacfb0bcc41c92b4a", "Package": "DspikeIn", "Type": "Package", "Title": "Estimating Absolute Abundance from Microbial Spike-in Controls", "Version": "1.3.0", "Authors@R": "c(\nperson(\"Mitra\", \"Ghotbi\", , \"mitra.ghotbi@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-9185-9993\")),\nperson(\"Marjan\", \"Ghotbi\", , \"ghotbi.marjan@gmail.com\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0003-4655-6445\"))\n)", "Description": "Provides a reproducible and modular workflow for absolute\nmicrobial quantification using spike-in controls. Supports both\nsingle spike-in taxa and synthetic microbial communities with\nuser-defined spike-in volumes and genome copy numbers.\nCompatible with 'phyloseq' and 'TreeSummarizedExperiment' (TSE)\ndata structures. 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across all samples?", "Pre_processing", "Spiked species and related parameters should be defined", "Calculate the percentage of spiked species retrieval", "spiked species retrieval is system-dependent", "Spiked species and related parameters for ITS", "Calculating Scaling Factors", "Convert relative counts to absolute counts", "Summary Stat", "Conclusion", "Abundance-based Core microbiome", "Data transform & Normalization", "Ridge plot", "Differential abundance (Single Pairwise)", "Differential abundance (Multilayer Pairwise)", "Turnover (Presence/absence analysis)", "Visualization", "Microbial dynamics & NetWork comparision", "Visualizes pairwise relationships between node-level metrics using a quadrant-based plot", "Comparision of node-level metrics", "To find neighbors of the target node", "Compute degree metrics and visualize the network", "Small-World Index Analysis", "DspikeIn volume protocol" ], "created": "2025-06-18 15:46:47", "modified": "2025-10-22 16:25:31", "commits": 4 } 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