Introduction to singleCellTK

In singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

The Single Cell Toolkit (SCTK) is an interactive scRNA-Seq analysis package that allows a user to upload raw scRNA-Seq count matrices and perform downstream scRNA-Seq analysis interactively through a web interface, or through a set of R functions through the command line. The package is written in R with a graphical user interface (GUI) written in Shiny. Users can perform analysis with modules for conducting quality control, clustering, batch correction, differential expression, pathway enrichment, and sample size calculator, all in a simple to use point and click interface. The toolkit also supports command line data processing, and results can be loaded into the GUI for additional exploration and downstream analysis.

Vignettes

Due to the range of features that are available in SCTK, we have prepared several vignettes to help you get started, which are all available at https://www.sctk.science.

• Installation/Introduction

Interactive Analysis

• Uploading Data
• Data Summary and Filtering
• Visualization and Clustering
• Batch Correction
• Differential Expression
• Pathway Activity Analysis
• Sample Size

R Console Analysis

• Processing and Visualizing Data in the Single Cell Toolkit
• Aligning and Quantifying scRNA-Seq Data

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singleCellTK documentation built on Nov. 8, 2020, 5:21 p.m.