We are looking to understand the current state-of-the-art and motivate new methods:
See Summary.ipynb for an overview of the analysis. Here's also the latest project review.
(Summary.html is a snapshot of Summary.ipynb with better rendering of the table of contents than Github's rendering of Summary.ipynb. It's also saved into gh-pages and hosted at www.hammerlab.org/immune-infiltrate-explorations/Summary.html. The table of contents is made by the TOC jupyter nbextension.)
Directories:
curated_data/
: data downloads. Some data is not in Git and is only in a Google bucket -- see README in curated_data
.data_engineering/
: some transformations of the dataevaluate_existing_methods/
: analysis to evaluate existing deconvolution methodshierarchical_models/
: new hierarchical classification modelsbehavior_of_rnaseq_data/
: analysis of how RNA-seq data behaves in comparison to microarray dataplots/
: generated figuresreference-extraction_writeup/reference_extraction.pdf
: an analysis of the reference extraction -- linked from Summary notebook