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Seurat (version 1.2.1)
Seurat : R toolkit for single cell genomics
Description
Seurat : R toolkit for single cell genomics
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Install
install.packages('Seurat')
Monthly Downloads
54,804
Version
1.2.1
License
GPL 3.0
Maintainer
Satija Lab
Last Published
October 5th, 2015
Functions in Seurat (1.2.1)
Search functions
diff.t.test
Differential expression testing using Student's t-test
average.expression
Averaged gene expression by identity class
average.pca
Average PCA scores by identity class
DBclust_dimension
Perform spectral density clustering on single cells
cluster.alpha
Probability of detection by identity class
cellPlot
Cell-cell scatter plot
buildClusterTree
Phylogenetic Analysis of Identity Classes
addImputedScore
Calculate imputed expression values
addMetaData
Add Metadata
batch.gene
Identify potential genes associated with batch effects
diffExp.test
Likelihood ratio test for zero-inflated data
doHeatMap
Gene expression heatmap
dim.plot
Dimensional reduction plot
dot.plot
Dot plot visualization
find_all_markers
Gene expression markers for all identity classes
find.markers
Gene expression markers of identity classes
feature.heatmap
Vizualization of multiple features
fetch.data
Access cellular data
feature.plot
Visualize 'features' on a dimensional reduction plot
doKMeans
K-Means Clustering
find.markers.node
Gene expression markers of identity classes defined by a phylogenetic clade
ica.plot
Plot ICA map
initial.mapping
Infer spatial origins for single cells
get.centroids
Get cell centroids
icHeatmap
Independent component heatmap
jackStraw
Determine statistical significance of PCA scores.
fit.gene.k
Build mixture models of gene expression
genePlot
Scatter plot of single cell data
ica
Run Independent Component Analysis on gene expression
icTopGenes
Find genes with highest ICA scores
plotClusterTree
Plot phylogenetic tree
pcTopGenes
Find genes with highest PCA scores
marker.test
ROC-based marker discovery
mean.var.plot
Identify variable genes
pca
Run Principal Component Analysis on gene expression
pca.sig.genes
Significant genes from a PCA
pcHeatmap
Principal component heatmap
pca.plot
Plot PCA map
Kclust_dimension
Perform spectral k-means clustering on single cells
jackStrawPlot
JackStraw Plot
set.all.ident
Switch identity class definition to another variable
set.ident
Set identity class information
project.pca
Project Principal Components Analysis onto full dataset
refined.mapping
Quantitative refinement of spatial inferences
run_tsne
Run t-distributed Stochastic Neighbor Embedding
rename.ident
Rename one identity class to another
plotNoiseModel
Visualize expression/dropout curve
seurat
The Seurat Class
setup
Setup Seurat object
subsetData
Return a subset of the Seurat object
print.pca
Print the results of a PCA analysis
tobit.test
Differential expression testing using Tobit models
which.cells
Identify matching cells
tsne.plot
Plot tSNE map
viz.ica
Visualize ICA genes
viz.pca
Visualize PCA genes
vlnPlot
Single cell violin plot