InSituType

Bioc removed

An R package for performing cell typing in SMI and other single cell data

v0.99.4 · MIT + file LICENSE

Release Lineage

Release history unavailable.

Description

Insitutype is an algorithm for performing cell typing in single cell spatial transcriptomics data, such as is generated by the CosMx platform. It can perform supervised cell typing from reference profiles, unsupervised clustering, or semi-supervised cell typing in which cells both reference cell types and de novo clusters are fit.

Code & tests

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Code

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Topics

Software › StatisticalMethod › Clustering

Software › Technology › SingleCell

Software › ResearchField › Transcriptomics

People

David Ross author maintainer
Patrick Danaher author
Zhi Yang author

At a glance

Version: 0.99.4
License: MIT + file LICENSE

Available on

CRAN r2u Bioconductor autoCRAN COPR

Dependencies

Depends

R (>= 3.5.0)

Imports

Matrix scales umap ggplot2 lsa irlba mclustsparseMatrixStatsBiocSummarizedExperimentBiocSingleCellExperimentBiocmethodsrlanggrDevicesgraphicsstatsutilsRcpp (>= 1.0.9)

Suggests

rmarkdown knitr testthat