Man pages for scGPS
A complete analysis of single cell subpopulations, from identifying subpopulations to analysing their relationship (scGPS = single cell Global Predictions of Subpopulation)

add_importadd_import
annotate_clustersannotate_clusters functionally annotates the identified...
bootstrap_parallelBootStrap runs for both scGPS training and prediction with...
bootstrap_predictionBootStrap runs for both scGPS training and prediction
calcDistCompute Euclidean distance matrix by rows
calcDistArmaCompute Euclidean distance matrix by rows
clusteringHC clustering for a number of resolutions
clustering_baggingHC clustering for a number of resolutions
CORE_baggingMain clustering SCORE (CORE V2.0) Stable Clustering at...
CORE_clusteringMain clustering CORE V2.0 updated
CORE_subclustersub_clustering (optional) after running CORE 'test'
day_2_cardio_cell_sampleOne of the two example single-cell count matrices to be used...
day_5_cardio_cell_sampleOne of the two example single-cell count matrices to be used...
distvecCompute Distance between two vectors
find_markersfind marker genes
find_optimal_stabilityFind the optimal cluster
find_stabilityCalculate stability index
mean_cppCalculate mean
new_scGPS_objectnew_scGPS_object
new_summarized_scGPS_objectnew_summarized_scGPS_object
PCAPCA
plot_COREPlot dendrogram tree for CORE result
plot_optimal_COREplot one single tree with the optimal clustering result
plot_reducedplot reduced data
predictingMain prediction function applying the optimal ElasticNet and...
PrinComp_cppPrincipal component analysis
rand_indexCalculate rand index
rcpp_Eucl_distance_NotParFunction to calculate Eucledean distance matrix without...
rcpp_parallel_distancedistance matrix using C++
reformat_LASSOsummarise bootstrap runs for Lasso model, from 'n' bootstraps
sub_clusteringsub_clustering for selected cells
subset_cppSubset a matrix
summary_accuracyget percent accuracy for Lasso model, from 'n' bootstraps
summary_devianceget percent deviance explained for Lasso model, from 'n'...
summary_prediction_lassoget percent deviance explained for Lasso model, from 'n'...
summary_prediction_ldaget percent deviance explained for LDA model, from 'n'...
top_varselect top variable genes
tp_cppTranspose a matrix
trainingMain model training function for finding the best model that...
training_gene_sampleInput gene list for training 'scGPS', e.g. differentially...
tSNEtSNE
var_cppCalculate variance
scGPS documentation built on Oct. 31, 2019, 2:23 a.m.