RCSL is an R toolkit for single-cell clustering and trajectory analysis using single-cell RNA-seq data.

This package can be installed through devtools in R:

```
$ R
> library("devtools")
> devtools::install_github("QinglinMei/RCSL")
```

Now RCSL can be loaded in R:

```
> library(RCSL)
```

The input of RCSL is a normalized data matrix with columns being cells and rows being genes in log(CPM+1), log(RPKM+1), log(TPM+1) or log(FPKM+1) format; or a data file in RDS format.

We provide an example script to run RCSL in *demo_RCSL.R*.

The nine functions of RCSL can also be run independently.

Function | Description
-----------|----------
`GenesFilter`

| Perform genes filtering.
`SimS`

| Calculate the initial similarity matrix S.
`NeigRepresent`

| Calculate the neighbor representation of cells.
`EstClusters`

| Estimate the optimal number of clusters C.
`BDSM`

| Learn the block-diagonal matrix B.
`PlotMST`

| Construct MST based on clustering results from RCSL.
`PlotPseudoTime`

| Infer the pseudo-temporal ordering of cells.
`getLineage`

| Infer the lineage based on the clustering results and the starting cell.
`PlotTrajectory`

| Plot the developmental trajectory based on the clustering results and the starting cell.

Load packages:

```
> library(RCSL)
> library(SingleCellExperiment)
> library(ggplot2)
> library(igraph)
```

Load Yan dataset:

```
> origData <- yan
> data <- logcounts(origData+1)
> label <- origData$cell_type1
> DataName <- "Yan"
```

Generating clustering result:

```
> res_RCSL <- RCSL(data)
```

Calculating Adjusted Rand Index:

```
> ARI_RCSL <- igraph::compare(res_RCSL$y, label, method = "adjusted.rand")
```

Trajectory analysis:

```
> label <- origData$cell_type1
> res_TrajecAnalysis <- TrajectoryAnalysis(res_RCSL$gfData, res_RCSL$drData, res_RCSL$S,
clustRes = res_RCSL$y, TrueLabel = label, startPoint = 1,
dataName = DataName)
```

Display the plot of constructed MST:

```
> res_TrajecAnalysis$MSTPlot
```

Display the plot of the pseudo-temporal ordering

```
> res_TrajecAnalysis$PseudoTimePlot
```

Display the plot of the inferred developmental trajectory

```
> res_TrajecAnalysis$TrajectoryPlot
```

A vignette in R Notebook format is available here

1) The RCSL package requires three extra packages: namely the *SingleCellExperiment* package (see https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html) to read the *SingleCellExperiment* object, the *igraph* package (see https://igraph.org/) to find the strongest connected components and the *ggplot2* package (see https://cran.r-project.org/web/packages/ggplot2/index.html) to plot the developmental trajectory and MST.
2) The data for the demonstration purpose in the directory *Data* was from https://hemberg-lab.github.io/scRNA.seq.datasets/. This data is stored in both RDS and text formats.

Please feel free to contact us if you have problems running our tool at meiqinglinkf@163.com.

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