rednaSander/omicsfm

Used to determine which cell types are enriched within gene lists. The package provides tools for testing enrichments within simple gene lists (such as human disease associated genes) and those resulting from differential expression studies. The package does not depend upon any particular Single Cell Transcriptome dataset and user defined datasets can be loaded in and used in the analyses.

PhenoSeq is a Gaussian diffusion model that generates scGPT RNA-seq embeddings conditioned on ViT-L microscopy imaging features. Given fluorescence microscopy images of a cell or well, it predicts a 512-dimensional scGPT embedding representing the transcriptomic state of individual cells — enabling…

Stack is a large-scale encoder-decoder foundation model for single-cell biology. It introduces a novel tabular attention architecture that enables both intra- and inter-cellular information flow, setting cell-by-gene matrix chunks as the basic input data unit.

C2S-Scale-Gemma-2-27B (GGUF Q8_0)

Nicheformer is a transformer-based model designed for understanding and predicting cellular niches and their interactions. The model uses masked language modeling to learn representations of cellular contexts and their relationships.

CASCADE: context-aware single-cell modelling links cellular programmes to patient-level disease phenotypes