scMoMaT

Muon — multimodal omics data analysis framework from the scverse ecosystem. Built on the MuData container for multi-modal single-cell experiments including CITE-seq, Multiome (RNA+ATAC), TEA-seq, and

2 shared topics • 1 shared operation

Use when working with SATURN for cross-species single-cell RNA-seq integration that combines AnnData count matrices with protein embedding TorchDicts. SATURN trains macrogene representations with k-me

2 shared topics • 1 shared operation

totalVI and MultiVI — deep generative models from scvi-tools for multi-modal single-cell integration. totalVI jointly models scRNA-seq and protein (CITE-seq) data via a variational autoencoder for den

2 shared topics • 1 shared operation

Giotto Suite — R toolkit for spatial multi-omics analysis at all scales and resolutions. Processes data from Visium, MERFISH, Xenium, CosMx, Slide-seq, CODEX, Stereo-seq, and other spatial technologie

2 shared topics

nf-core — community-curated Nextflow pipeline framework with 100+ production bioinformatics pipelines. Provides CLI tools for listing, launching, downloading, creating, and linting pipelines; managing

2 shared topics