flotilla is a Python package for visualizing transcriptome (RNA expression) data from hundreds of samples. We include utilities to perform common tasks on these large data matrices, including:
- Dimensionality reduction
- Classification and Regression
- Outlier detection
- Network graphs from covariance
- Hierarchical clustering
And common tasks for biological data including:
- Renaming database features to gene symbols
- Coloring/marking samples based on experimental phenotype
- Removing poor-quality samples (technical outliers)
Finally, flotilla is a platform for active collaboration between bioinformatics scientists and traditional "wet lab" scientists. Leveraging interactive widgets in the IPython Notebook, we have created tools for simple and streamlined data exploration including:
- Subsetting sample groups and feature (genes/splicing events) groups
- Dynamically adjusting parameters for analysis
- Integrating external lists of features from the web or local files
These empower the "wet lab" scientists to ask questions on their own and gives bioniformatics scientists a platform and share their analysis tools.
What flotilla is not -----------------------
flotilla is not a genomics pipeline. We expect that you have already generated data tables for gene expression, isoform expression and metadata. flotilla only makes it easy to integrate all those data parts together once you have the pieces.