Welcome to SpatialOncology’s documentation!

This documentations contains the resources for multiplexed single-cell spatial analysis.

Cytometry Analysis Tutorials

• Data scientist’s primer to analysis of mass cytometry data https://biosurf.org/cytof_data_scientist.html

Data Transformations

• ArcSinh transformation, with a co-factor of 5

• Log transformation

BEC Algorithms

• Batch Effects Evaluation and Correction https://biosurf.org/cyCombine_CyTOF_1panel.html

• ComBat https://github.com/epigenelabs/pyComBat

• cyCombine https://github.com/biosurf/cyCombine

• CytoNorm https://github.com/saeyslab/CytoNorm

• CytofRUV https://github.com/mtrussart/CytofRUV

CD Algorithms

• PhenoGraph https://github.com/jacoblevine/PhenoGraph

• Leiden https://github.com/vtraag/leidenalg

• FastPG https://github.com/sararselitsky/FastPG

Dimension Reduction

• PCA, linearly map data from high dimensional space to a lower dimensional space

• t-SNE https://scikit-learn.org/stable/modules/generated/sklearn.manifold.TSNE.html

• UMAP https://github.com/lmcinnes/umap