Pinned Repositories
DOMINO
Network-based module discovery algorithm with high rate of empirically-validated term calls
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
INTEND
INTEND (IntegratioN of Transcriptomic and EpigeNomic Data), a novel algorithm for integrating gene expression and DNA methylation datasets covering disjoint sets of samples
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
Recycler
This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye Rozov, Aya Brown Kav, David Bogumil, Naama Shterzer, Eran Halperin, Itzhak Mizrahi, and Ron Shamir
SCAPP
SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-021-01068-z
syncmer_mapping
Implementations of syncmer-based long read mappers
Ron Shamir's Lab's Repositories
Shamir-Lab/Recycler
This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye Rozov, Aya Brown Kav, David Bogumil, Naama Shterzer, Eran Halperin, Itzhak Mizrahi, and Ron Shamir
Shamir-Lab/SCAPP
SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-021-01068-z
Shamir-Lab/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
Shamir-Lab/Multi-Omics-Cancer-Benchmark
Shamir-Lab/NEMO
Shamir-Lab/DOMINO
Network-based module discovery algorithm with high rate of empirically-validated term calls
Shamir-Lab/PRODIGY
Personalized prioritization of driver genes in cancer
Shamir-Lab/INTEND
INTEND (IntegratioN of Transcriptomic and EpigeNomic Data), a novel algorithm for integrating gene expression and DNA methylation datasets covering disjoint sets of samples
Shamir-Lab/MONET
MONET
Shamir-Lab/syncmer_mapping
Implementations of syncmer-based long read mappers
Shamir-Lab/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
Shamir-Lab/DOCKS
Java code for DOCKS algorithm
Shamir-Lab/3CAC
Shamir-Lab/4CAC
Shamir-Lab/AdaOrder
Shamir-Lab/clustering_echo_covid
using k-prototype algorithm on mixed-type medical data
Shamir-Lab/domino_web
Shamir-Lab/EMP
EMpirical Pipeline for correcting GO terms obtained by network-based module discovery algorithms.
Shamir-Lab/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
Shamir-Lab/Logrank-Inaccuracies
Shamir-Lab/MSP_UHS
Shamir-Lab/EMP-benchmark
EMP-based benchmark for Network-based discovery of activity modules
Shamir-Lab/ABXAppropriatenessML
Prediction of ABX appropriateness in ICU inpatients
Shamir-Lab/covid19-mnews
Shamir-Lab/DGerbil
A fast and memory-efficient k-mer counter with GPU-support
Shamir-Lab/EnhancerSilencerDL
Codebase for inferring single nucleotide activation and repression maps using deep-learning
Shamir-Lab/FRIGATE
Frigate - Feature ranking for clustering using game theory
Shamir-Lab/PRS-imputation-panels
Shamir-Lab/SPRINT
This R code reproduces the results presented in: "Personalized prediction of adverse heart and kidney events using pre-enrollment and time course data from SPRINT and ACCORD trials"
Shamir-Lab/StatTheGit4TAU
Maintain GitHub Stats for More than 14 Days