Bioconductor AnnotationDbi

ComplexHeatmap — R/Bioconductor package for creating highly customizable heatmaps with complex annotations. Supports row/column splitting, multiple annotation tracks (bar, box, point, histogram), Onco

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scArches (Single-cell Architecture Surgery) — Python toolkit for reference-based single-cell data integration via transfer learning. Maps query datasets into pre-trained reference atlases using archit

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scFoundation — large-scale pretrained foundation model for single-cell transcriptomics built on the xTrimo transformer architecture. Trained on ~50 million human single-cell profiles, scFoundation gen

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STAR-Fusion — detects candidate fusion transcripts from RNA-seq data using STAR alignments and the FusionInspector validation framework. Integrates with CTAT genome resource libraries for comprehensiv

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Trinity — de novo transcriptome assembler for RNA-seq data. Reconstructs full-length transcript isoforms without a reference genome using three sequential modules: Inchworm (greedy k-mer assembly), Ch

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