# Robust Clustering of Single Cell RNA-Seq Data

## Documentation for package ‘robustSingleCell’ version 0.1.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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