GenePattern (original) (raw)

Features

Powerful genomics tools in a user-friendly interface

GenePattern provides hundreds of analytical tools for the analysis of gene expression (RNA-seq and microarray), sequence variation and copy number, proteomic, flow cytometry, and network analysis. These tools are all available through a Web interface with no programming experience required.

GenePattern Notebook

The GenePattern Notebook environment extends the Jupyter Notebook system, allowing researchers to create documents that interleave formatted text, graphics and other multimedia, executable code, and GenePattern analyses, creating a single "research narrative" that puts scientific discussion and analyses in the same place.

Analysis Pipelines

GenePattern pipelines allow you to capture, automate, and share the complex series of steps required to analyze genomic data. By providing a way to create and distribute an entire computational analysis methodology in a single executable script, pipelines enable a form of in silico reproducible research.

Reproducible Research

Published research, particularly in silico research, should contain sufficient information to completely reproduce the research results. By capturing the analysis methods, parameters, and data used to produce the research results, GenePattern pipelines enable reproducible research. By versioning every pipeline and its methods, GenePattern ensures that each version of a pipeline (and its results) remain static, even as your research and the pipeline continue to evolve.

Programming Environment

GenePattern provides a simple application interface that gives users access to computational analysis methods and tools, regardless of their computational experience. GenePattern also provides a programmatic interface that makes those analysis modules available to computational biologists and developers from Java, MATLAB, and R.