shamir-lab Goto Github PK

3cac

4cac

abxappropriatenessml

Prediction of ABX appropriateness in ICU inpatients

adaorder

adeptus-2.0

Server side (all python code) of the ADEPTUS webtool

barcode

an implementation of the BARCODE algorithm in C

clustering_echo_covid

using k-prototype algorithm on mixed-type medical data

covid19-mnews

ct-focs

Codebase for CT-FOCS, a new method for inferring cell type-specific enhancer-promoter (EP) links and for integrative analysis of EP links

dgerbil

A fast and memory-efficient k-mer counter with GPU-support

docks

Java code for DOCKS algorithm

domino

Network-based module discovery algorithm with high rate of empirically-validated term calls

domino_web

emp

EMpirical Pipeline for correcting GO terms obtained by network-based module discovery algorithms.

emp-benchmark

EMP-based benchmark for Network-based discovery of activity modules

enhancersilencerdl

Codebase for inferring single nucleotide activation and repression maps using deep-learning

faucet

This is the codebase for Faucet, described in our manuscript: https://academic.oup.com/bioinformatics/article/34/1/147/4004871, by Roye Rozov, Gil Goldshlager, Eran Halperin, and Ron Shamir

focs

Codebase for FOCS, a new method for inferring enhancer-promoter (E-P) links and for integrative analysis of E-P links

frigate

Frigate - Feature ranking for clustering using game theory

genepark

GENEPARK is a large study that aimed for finding blood-based biomarkers Parkinson's disease. Here we provide the R code for reproducing the main results of the project.

intend

INTEND (IntegratioN of Transcriptomic and EpigeNomic Data), a novel algorithm for integrating gene expression and DNA methylation datasets covering disjoint sets of samples

karyotype-reconstruction

An ILP based algorithm to reconstruct karyotypes, and a karyotype simulator. The algorithm is described in the manuscript bioRxiv 152447; doi: https://doi.org/10.1101/152447

logrank-inaccuracies

monet

MONET

msp_uhs

multi-omics-cancer-benchmark

nemo

plasclass

A tool to classify sequences of plasmid or chromosomal origin. A paper describing this tool is available at: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007781

prodigy

Personalized prioritization of driver genes in cancer

prs-imputation-panels