# _scGPS_ - Single Cell Global fate Potential of Subpopulations
<img src="man/figures/scGPSlogo.png" width="200px">
The _scGPS_ package website is available at: https://imb-computational-genomics-lab.github.io/scGPS/index.html
The usage instruction can be found at: https://imb-computational-genomics-lab.github.io/scGPS/articles/vignette.html
## _scGPS_ general description
_scGPS_ is a complete single cell RNA analysis framework from decomposing a mixed population into clusters (_SCORE_) to analysing the relationship between clusters (_scGPS_). _scGPS_ also performs unsupervised selection of predictive genes defining a subpopulation and/or driving transition between subpopulations.
The package implements two new algorithms _SCORE_ and _scGPS_.
Key features of the _SCORE_ clustering algorithm
- Unsupervised (no prior number of clusters), stable (with automated selection of stability and resolution parameters through scanning a range of search windows for each run, together with a boostrapping aggregation approach to determine stable clusters), fast (with Rcpp implementation)
- _SCORE_ first builds a reference cluster (the highest resolution) and then runs iterative clustering through 40 windows (or more) in the dendrogram
- Resolution is quantified as the divergence from reference by applying adjusted Rand index
- Stability is the proportional to the number of executive runs without Rand index change while changing the cluster search space
- Optimal resolution is the combination of: stable and high resolution
- Bagging algorithm (bootstrap aggregation) can detect a rare subpopulation, which appears multiple times during different decision tree runs
Key features of the _scGPS_ algorithm
- Estimates transition scores between any two subpopulations
- _scGPS_ prediction model is based on Elastic Net procedure, which enables to select predictive genes and train interpretable models to predict each subpopulation
- Genes identified by _scGPS_ perform better than known gene markers in predicting cell subpopulations
- Transition scores are percents of target cells classified as the same class to the original subpopulation
- For cell subtype comparision, transition scores are similarity between two subpopulations
- The scores are average values from 100 bootstrap runs
- For comparison, a non-shrinkage procedure with linear discriminant analysis (LDA) is used
## _scGPS_ workflow
_scGPS_ takes scRNA expression dataset(s) from one or more unknown sample(s) to find subpopulations and relationship between these subpopulations. The input dataset(s) contains mixed, heterogeous cells. _scGPS_ first uses _SCORE_ (or _CORE_ V2.0) to identify homogenous subpopulations. _scGPS_ contains a number of functions to verify the subpopulations identified by _SCORE_ (e.g. functions to compare with results from PCA, tSNE and the imputation method CIDR). _scGPS_ also has options to find gene markers that distinguish a subpopulation from the remaining cells and performs pathway enrichment analysis to annotate subpopulation. In the second stage, _scGPS_ applies a machine learning procedure to select optimal gene predictors and to build prediction models that can estimate between-subpopulation transition scores, which are the probability of cells from one subpopulation that can likely transition to the other subpopulation.
<img src="man/figures/packagePlan.png" width="450px"> <br>
Figure 1. scGPS workflow. Yellow boxes show inputs, and green boxes show main scGPS analysis.