PhyloDiver [Webtool][GitHub]  
An interactive tool for visualizing and exploring evolutionary phylogenies constructed from analyses of genetic variations in tumor samples. This tool was designed to simultaneously enable end-users to examine mutation histories while maintaining sample proportions of different subclone populations.

PhyloFlow [GitHub] [CWL] 
A workflow that packages command line tools from the field of cancer phylogeny into the core steps for computing phylogenetic trees and making the outputs compatible with PhyloDiver

TraRe [R]
An algorithm to identify rewired regulatory networks from RNA-seq data. It does this by finding gene regulatory networks (GRN) modules; scoring these modules via a rewiring test; and then visualizing condition-specific GRN deregulation.

DRaWR [CRAN Package] [R] [Python]
An algorithm to rank genes and gene properties (e.g. pathway annotations) related to a given gene set using discriminative random walks with restart on a heterogeneous network of biological information.

KnockNet [Python]
Multi-class convolutional neural network that models gene knockdowns from paired transcriptional states across many cellular contexts.

cis-Metalysis [C++]
A powerful framework for meta-analysis of annotation – condition associations across multiple conditions. cis-Metalysis specifically searches for significant combinations of computational transcription factor binding motifs common across gene sets from multiple related cellular states.

KnowEnG Knowledge Network [Contents] 
Heterogeneous network of biological knowledge that contains relationships/interactions between and properties/annotations of genes and proteins. This resource harmonizes data from dozens of public databases, covering 20 species and nearly 500M relationships, to facilitate knowledge-guided analysis of genomic datasets.

KN_Builder [Python] [Launcher] [Docker] [Documentation]
Automated, Dockerized, parallelized pipeline that downloads, parses, harmonizes, and reformats the information from public biological databases for the KnowEnG Knowledge Network.

KN Utilities
Softwares that empower users of the KnowEnG Knowledge Network
– to download a specific portion, KN_Fetcher [Python] [Docker] [CWL]
– or to map gene and protein names to standard identifiers, KN_Mapper [Python] [Docker] [CWL].

KnowEnG Analytic Pipelines [CWL]
A Common Workflow Language description of the knowledge-guided analyses produced by KnowEnG, useful for building workflows in external compute environments.