ggalign - A 'ggplot2' Extension for Composable Visualization
A 'ggplot2' extension providing an integrative framework for composable visualization, enabling the creation of complex multi-plot layouts such as insets, circular arrangements, and multi-panel compositions. Built on the grammar of graphics, it offers tools to align, stack, and nest plots, simplifying the construction of richly annotated figures for high-dimensional data contexts—such as genomics, transcriptomics, and microbiome studies—by making it easy to link related plots, overlay clustering results, or highlight shared patterns.
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complex-heatmapsdendrogramdendrogram-heatmapggplotggplot-extensionggplot2heatmapheatmap-visualizationheatmapsmarginal-plotsoncoplotoncoprinttanglegramupsetupsetplot
7.13 score 405 stars 96 scripts 580 downloadsgeokit - Tools for Accessing and Working with the Gene Expression Omnibus (GEO)
Provides a tidy and fast R interface to the NCBI Gene Expression Omnibus (GEO) database. Functions are included to query, download, and parse GEO metadata and expression data, making it easier to integrate GEO datasets into downstream analyses and workflows.
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rustcargo
5.48 score 6 stars 7 scriptsrsahmi - Single-Cell Analysis of Host-Microbiome Interactions
A computational resource designed to accurately detect microbial nucleic acids while filtering out contaminants and false-positive taxonomic assignments from standard transcriptomic sequencing of mammalian tissues. For more details, see Ghaddar (2023) <doi:10.1038/s43588-023-00507-1>. This implementation leverages rust for fast and systematic microbial signal recovery and denoising from host tissue genomic sequencing.
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microbiomesahmisingle-cellrustcargo
4.04 score 11 stars 54 downloadsmire - Microbiome Integrated Reconstruction and Estimation
An integrated framework for microbiome reconstruction from sequencing data. It leverages tools like Kraken2 for taxonomic classification and combines cell barcodes, UMIs, and k-mer-based quantification to reconstruct microbial signals. Designed for both bulk and single-cell sequencing data, the package enables taxonomic and quantitative profiling of microbial communities.
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rustcargo
2.90 score 4 stars 3 scripts