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    Downloadable software tools

     

    The research projects performed by groups in the Center involve the construction of new software tools. Invention of new approaches or computational procedures are accompanied by development of software tools and testing them on the problem data. Tools that prove useful are made available to the biomedical research world as downloadable tools/databases, or as online services.

     

     

    List of downloadable software tools:

     

    Group

    Tool name

    Purpose

    Shamir/Elkon

    Expander

    Gene expression and deep sequencing data analysis

    Mayrose/ Pupko

    rate4site

    Detection of  conserved amino-acid sites

    Mayrose

    Chrom-Evol

    Analysis of changes in chromosome number

    E.Halperin

    LAMP

    Admixture mapping

    E.Halperin

    Re-FACTor

    Estimating cell type composition

    Shamir

    Hyden

    Design of highly degenerate primers

    Gat-Viks

    Imm-Quant

    Studying the physiology of immune-cell types in complex tissues

    Halperin

    GLINT

    EWAS analysis.

    Shamir

    Amadeus & Allegro

    Detect regulatory motifs

    Sharan

    ANAT

    Biological network analysis

    Shamir

    Matisse

    Module analysis via topology of interactions and similarity sets

    Halperin

    ALBI and FIESTA

    Construct confidence intervals for heritability estimates

    Shamir

    Dicer

    Integrative analysis of biological networks

    Shamir

    Recycler

    Extracting circular elements from deep sequencing data

    Shomron

    miRNA-key

    Differential expression of miRNAs from NGS

    Shamir

    ModMap

    Joint analysis of two biological networks

    Gat-Viks

    VoCAL

    Infer the quantities of immune cell types, and uncover DNA loci

    Shamir

    TWIGS

    3-way module Inference

    Tuller

    RFMapp

    Ribosome flow model 

    Tuller

    MTDR 

    Calculate translation efficiency index

    Tuller

    stAIcalc

    Calculate tRNA adaptation index 

    Tuller

    Transim

    Translation initiation and elongation model

    Tuller

    Chimera 

     
    Analyze gene expression using the genetic code

    Gat-Viks

    POEM

    Identify pairwise eQTL effects on gene modules 

    Gat-Viks

    GEMOT

    Construct  causative model of trait–trait connections

    Gat-Viks

    DyVer

    Dynamic Variant Effect on Response

     

    Shamir

    PROMO

    Analysis of large multi-omic and clinical datasets

     

     

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