Articles

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Short examples on Bioconductor data; these are the package vignettes.

Introduction to PhiSpace

PhiSpace ST for spatial transcriptomics

PhiSpace multiomics: using PhiSpace for single-cell multiomics

Using bulk or single-cell RNA-seq references to annotate single-cell multiomics queries.

Getting Started: mapping scRNA-seq to bulk RNA-seq atlas

Perturb-seq: using bulk reference to evaluate strengths of CRISPRa gene perturbation

Bimodal annotation using CITE-seq

Annotation of scATAC-seq using scRNA-seq reference

PhiSpace ST: using PhiSpace for spatial transcriptomics

Platform-agnostic cell state annotation of ST queries using scRNA-seq references.

Visium: cell type deconvolution for multi-cellular spots

CosMx: discovery of divergent cell states in lung cancer microenvironment

Stereo-seq: lineage commitment of AML cells

Stored PhiSpace models

Training a model once and applying it to new queries without the reference.

Pretrain PhiSpace models: train once, annotate later