This repository contains software for analysis of gene expression data from single-cell RNA sequencing developed at Chan-Zuckerberg Initiative.
This code is at a prototype, pre-alpha stage. It is hoped that it can be useful in its current form, but it is likely that it contains bugs or other errors or limitations that impact its ability to give meaningful results. In addition, a validation of this code has not been performed. This prototype code is released in open source form with an MIT license.
Follow one of the links below for more information.
Visualizing and analyzing using the http server
Starting a run and analyzing results using the Python API
Reference information for the Python API
Information useful if you plan to use the ExpressionMatrix2
Python API. This allows you to invoke
ExpressionMatrix2 functionality from Python code.
Building from source
Explains how to build the ExpressionMatrix2
software from source code. For most applications you
will not need to do this, and you can instead use
pre-built code from a published release
available from GitHub.
Programming notes
Information that could be useful if you plan to study
or modify the ExpressionMatrix2 C++ code.
Case study 1
Illustrates use of the ExpressionMatrix2 software
on a real life single-cell RNA sequencing data set.
LSH slides
This presentation describes the computational techniques, based on
Locality Sensitive Hashing, than enable
scaling up to large numbers of cells.