flotilla — An open-source toolkit for single-cell RNA-seq data analysis
In [1]:
import css_styling
Why single cells?
Goals of flotilla
Test-drive
Single cell transcriptomics stand to change the way biologists look at heterogeneity in gene expression and the types of questions they will want to ask.
How is gene expression varied and how does gene expression co-vary?
Are there cell sub-populations?
What genes create the largest diffence between two groups of cells?
As computation and large-scale biology becomes more demanded, more than ever bioinformaticians will be called on to interpret and describe to the data that biologists create.
With this increased demand for bioinformaticians' time, there must be reliable and scalable solutions for processing and sharing data, analysis and methods.
Live-coding in meetings and presentations.
Data sharing.
Replication in multiple computation environments.
flotilla.
The docker Virtual Machine is re-built on Docker Hub with every change to flotilla. Start a container with flotilla installed and an iPython notebook running with:
sudo docker run -v ${HOME}/flotilla_projects:/root/flotilla_projects \
-v ${HOME}/flotilla_notebooks:/root/home/ipython \
-it -P -p 8888 \
mlovci/flotilla:dev # ( or mlovci/flotilla:latest )
Where -v mounts host directories in the VM for read/write.
There is also a web-start tool for Mac OS X users that have already installed docker:
curl https://raw.githubusercontent.com/\
YeoLab/flotilla/dev/docker/start_docker.py |python