Tuesday, 25 March 2014

Monocle is a R toolkit for analyzing single cell expression experiments

---------- Forwarded message ----------
From: Cole Trapnell <cole cs.umd.edu>
Date: Mon, Mar 24, 2014 at 11:51 PM
Subject: [Bowtie-bio-announce] Monocle 0.99.0
To: bowtie-bio-announce lists.sourceforge.net

I am proud to announce the first release of the Monocle analysis toolkit for single-cell RNA-Seq and qPCR.  Monocle performs differential expression and time series analysis for single-cell expression experiments.  You can read about Monocle and its “pseudo time” analysis of biological processes in the paper, which just appeared on Nature Biotech’s AOP list:


The Monocle source code and support site is also live:


I hope you will consider using Monocle for your single-cell expression analysis workflow!  Please report any issues on the new Monocle google group:


Note that Monocle is currently considered an ALPHA release - new features and interfaces changes will be coming in future releases, along with significant new functionality. The release announcement for Monocle v 0.99.0 is below.



0.99.0 release - 3/23/2014

The first public release of Monocle is now available for download. Monocle is a toolkit for analyzing single cell expression experiments. It runs on the R statistical computing platform.

Monocle takes as input a matrix of gene or transcript expression values, along with information about each cell in the experiment, and some annotation about each gene/transcript, both provided as simple tables. It is designed for single-cell RNA-Seq experiments, but in principle Monocle can be used with other data types such as qPCR. For RNA-Seq, you can useCufflinks to estimate your expression values.

This software is a work in progress - it is a beta release, and new features will continue to be added over the next couple of weeks. To suggest a feature or report a bug, please post your comments on the Monocle user's group.

Cole Trapnell


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