Marker-Based Cell Type Purification for Single-Cell Sequencing Data
Overview
A common bioinformatics task in single-cell data analysis is to purify a cell type or cell population of interest from heterogeneous datasets. 'scGate' automatizes marker-based purification of specific cell populations, without requiring training data or reference gene expression profiles. Briefly, 'scGate' takes as input: i) a gene expression matrix stored in a 'Seurat' object and ii) a “gating model” (GM), consisting of a set of marker genes that define the cell population of interest. The GM can be as simple as a single marker gene, or a combination of positive and negative markers. More complex GMs can be constructed in a hierarchical fashion, akin to gating strategies employed in flow cytometry. 'scGate' evaluates the strength of signature marker expression in each cell using the rank-based method 'UCell', and then performs k-nearest neighbor (kNN) smoothing by calculating the mean 'UCell' score across neighboring cells. kNN-smoothing aims at compensating for the large degree of sparsity in scRNA-seq data. Finally, a universal threshold over kNN-smoothed signature scores is applied in binary decision trees generated from the user-provided gating model, to annotate cells as either “pure” or “impure”, with respect to the cell population of interest. See the related publication Andreatta et al. (2022) doi:10.1093/bioinformatics/btac141.
Install
Health
- OK13 OK2026-08-04
- NOTE12 OK, 1 NOTE2026-08-01
- OK13 OK2026-06-09
- ERROR12 OK, 1 ERROR2026-06-08
- OK13 OK2026-05-10
Show 6 earlier changesHide 6 earlier changes
- ERROR12 OK, 1 ERROR2026-05-03
- OK14 OK2026-04-21
- ERROR13 OK, 1 ERROR2026-04-19
- OK14 OK2026-04-10
- ERROR13 OK, 1 ERROR2026-04-09
- OK14 OK2026-03-10
Documentation
- Help pages
- 13
- Examples that run
- 45%5 run in a plain check · 4 only when donttest examples are enabled (R CMD check --as-cran) · 2 never run
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
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Repository
- PRs merged (all time)
- 100%
- Median days to close, 50 most recently updated closed issues
- 27
- Median days to close, 50 most recently updated closed PRs
- 0
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Checks run against github.com/carmonalab/scgate on 2026-10-18.
No development-tooling practices detected in the upstream repository.
Dependencies
Installing scGate adds 136 packages (82 with compiled code, 129 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, ggplot2 6.0 MB. 2 more not on CRAN are not measured.
Code & Tests
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People & History
Package metadata
- First published
- 2022-12-20
- Total releases
- 5 / 4 yrs
- License
- GPL-3 OSI
- Minimum R
- ≥ 4.3.0
- Bundled data
- 1.5 MB / 2 files
- Download size
- 1.5 MB
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