Robust Clustering of Single Cell RNA-Seq Data


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Documentation for package ‘robustSingleCell’ version 0.1.1

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add.confounder.variables Add Confounder Variables
assess.cluster.similarity Assess Cluster Similarity
cell.cycle.score Compute Cell Cycle Score
cluster.analysis Distributed Clustering Analysis
controlled.mean.score Compute Controlled Activation Score
download_LCMV Download Example Dataset
filter_cluster_data Remove selected clusters
find_neighbors K Nearest Neighbour Search
get.cluster.names Get/Set Cluster Names by Marker Gene Expression
get.robust.cluster.similarity Get Robust Cluster Similarity
get.robust.markers Get Robust Marker
get.variable.genes Identify Highly Variable Genes
initialize.project Intialize the Project Environment
mitochondrial.score Compute Mitochondrial Score
PCA Parallelized PCA Analysis
plot_contour_overlay_tSNE Plot Gene Expression on tSNE
plot_pair_scatter Plot Pairwise Gene Scatter Plot
plot_PCA Plot PCA results
plot_simple_heatmap Plot heatmap
read.data Read and Preprocess Data
read.preclustered.datasets Read Preclustered Datasets
read_10x_data Read 10X Data
ribosomal.score Compute Ribosomal Score
Rphenograph RphenoGraph clustering
run_tSNE Perform tSNE Analyses
set.cluster.names Get/Set Cluster Names by Marker Gene Expression
setup_LCMV_example Set up LCMV1 example
setup_pooled_env Set up the pooled environment
summarize Differential Expression and Figure Generation
visualize.cluster.cors.heatmaps Visualize Correlation
visualize.cluster.similarity.stats Plot Similarity Results