SnapHiC

SingleCellExperiment — core R/Bioconductor container class for single-cell genomics data. Stores assays (counts, logcounts, normalized), cell metadata (colData), gene metadata (rowData), dimensionalit

2 shared topics • 2 shared operations

Evo — genomic foundation model for DNA sequence modeling at single-nucleotide resolution. Uses StripedHyena architecture (7B parameters) trained on 2.7M prokaryotic and phage genomes (OpenGenome datas

2 shared topics • 1 shared operation

Geneformer — transformer-based foundation model pretrained on ~30 million single-cell transcriptomes for context-specific gene network analysis. Supports fine-tuning for cell type classification, gene

2 shared topics • 1 shared operation

Loom — HDF5-based file format and Python library (loompy) for storing and accessing large single-cell RNA-seq datasets. Supports sparse/dense matrices, row attributes (genes/features), column attribut

2 shared topics • 1 shared operation

stLearn — spatial transcriptomics analysis in Python integrating gene expression with tissue morphology. Provides SME (spatial morphological gene expression) normalization, spatial clustering, spatial

2 shared topics • 1 shared operation