Snakemake workflow designed to annotate VCF files withe SnpEff / SniSift
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Feb 18, 2021 - Python
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msigdb
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Integration of pathway-related information from MSigDB in BEL
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Nov 18, 2020 - Python
SpatialTranscriptFormer: A biologically-informed transformer architecture for spatial transcriptomics. Features Quad-Flow Interaction (P↔P, P↔H, H→P, H↔H) and a pathway bottleneck using MSigDB Hallmarks. Integrated with pathology foundation models (CTransPath/Phikon).
bioinformatics deep-learning computational-biology gene-expression pytorch transformer transcriptomics msigdb histology digital-pathology pathology explainable-ai multimodal spatial-transcriptomics biological-pathways foundation-models
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Jul 30, 2026 - Python
Knowledge or sparsity? A controlled test of gene set masks in an interpretable single-cell VAE.
benchmark bioinformatics gene-sets deep-learning computational-biology pytorch scrna-seq single-cell msigdb pathway-analysis variational-autoencoder single-cell-rna-seq explainable-ai interpretable-machine-learning prior-knowledge interferon pbmc negative-controls biologically-informed-neural-networks
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Oct 22, 2026 - Python
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