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Q: What is this?
A: SC3 is an interactive tool for the unsupervised clustering of cells from single cell RNA-Seq experiments. SC3 main page is on BioConductor.

Q: How to install/run SC3?
A: Please follow the SC3 manual from its BioConductor page.

Q: Where can I report bugs, comments, issues or suggestions?
A: Please use this page.

Q: Where can I ask questions about SC3?
A: Please use this page.

Q: Is SC3 published?
A: SC3 manuscript is under review, but also available on bioRxiv.

Q: What is SC3 licence?
A: GPL-3

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Version

Version

1.1.4

License

GPL-3

Issues

Pull Requests

Stars

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Maintainer

Vladimir Kiselev

Last Published

February 15th, 2017

Functions in SC3 (1.1.4)

get_data

Import expression matrix
StabilityIndex

Calculate the stability index of the obtained clusters when changing k
iwanthue

Generate a colour palette by k-means clustering of LAB colour space.
get_outl_cells

Find cell outliers
get_de_genes

Find differentially expressed genes
transformation

Distance matrix transformation
treutlein

Single cell RNA-Seq data extracted from a publication by Treutlein et al.
support_vector_machines

Run support vector machines (SVM) prediction
calculate_distance

Calculate a distance matrix
cell_filter

Cell filter
sc3

SC3 main function
sc3_interactive

SC3 interactive function
get_marker_genes

Find marker genes
gene_filter

Gene filter
consensus_matrix

Calculate consensus matrix
swatch

Plot colour swatches for a vector of colours
norm_laplacian

Graph Laplacian calculation