Software

The following repositories contain software related to the CURE BD4BH project that is available for download.

SQUID -- detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data

Split Sequence Bloom Tree (SSBT) -- indexes a set of short-read sequencing experiments and then allows them to be queried quickly for a given sequence

Weighted simplicial complex unmixing code for use with Matlab

Tree Unmixing Structural Variants -- Python code for deconvolution and phylogeny inference using structural variants and copy number segments

Code implementing methods for pooling bulk and single cell data for copy number deconvolution

DeepPhe analytic software -- extracts information from plaintext documents, summarizes information for cancers and tumors across multiple documents, and writes results to a Neo4j database

Spectral clustering of differentially expressed genes

Cost-sensitive classifier

Breast cancer treatment response