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https://github.com/boyden/NuHTC.git
Software nuclei instance segmentation and classification framework based on hybrid task cascade.
Proper citation: NuHTC (RRID:SCR_028227) Copy
https://github.com/moothes/MICE
Source code for work submitted to journal. Multimodal foundation model for pan-cancer prognosis prediction developed on 14,468 patients across 30 cancer types using a collaborative multi-expert architecture that retains unique signals from each modality while modeling their interactions.
Proper citation: MICE (RRID:SCR_028347) Copy
https://github.com/ShixiangWang/sigflow
Software automated and comprehensive pipeline for cancer genome mutational signature analysis. Provides one-stop solution for de novo signature extraction, reference signature fitting, signature stability analysis, sample clustering based on signature exposure in different types of genome DNA alterations including single base substitution, doublet base substitution, small insertion and deletion and copy number alteration. It can auto-extract mutational signatures, fit mutation data to all/specified COSMIC reference signatures (SBS/DBS/INDEL) and run bootstrapping analysis for studying signature stability.
Proper citation: SigFlow (RRID:SCR_028486) Copy
https://github.com/junjunlab/GseaVis
Software R package for enhanced visualization of gene set enrichment analysis in biomedicine. Used to visualize Gene Set Enrichment Analysis (GSEA) results.
Proper citation: GseaVis (RRID:SCR_028574) Copy
https://github.com/XSLiuLab/TLimmuno2
Software tool for predicting MHC class II antigen immunogenicity through transfer learning. Used to predict whether epitope-MHC class II complex can elicit T cell response.
Proper citation: TLimmuno2 (RRID:SCR_028675) Copy
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