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alignontology

Code for aligning two ontologies. Originally used in "A gene ontology inferred from molecular networks" doi:10.1038/nbt.2463

clixo-1.0

CliXO algorithm re-implemented

dbl-visualization

dcell

DCell browser and gene deletion simulator

ddot

Toolkit for constructing, analyzing, and visualizing data-driven ontologies

deiva_github

DEIVA prototype, implemented in Shiny

dotfiles

various configuration files including .gitconfig, .vimrc and .screenrc

drugcell

A visible neural network model for drug response prediction

genome-research-edger-deseq2

Generate edgeR- and DESeq2-flavored input files for DEIVA

hisig

Enrichment analysis for nested and overlapping gene sets

hiview

HiView of DNA Damage Response Assemblies Map (DDRAM)

ldl

Learning Deep Learning

microbiome-metabolome-curated-data

AK fork of Muller, E., Algavi, Y.M. & Borenstein, E. The gut microbiome-metabolome dataset collection: a curated resource for integrative meta-analysis. npj Biofilms Microbiomes 8, 79 (2022). https://doi.org/10.1038/s41522-022-00345-5

nest_drugcell_sdp

shap

A game theoretic approach to explain the output of any machine learning model.