Downloadable & Online Tools

updated: 04.02.2021

  • Downloadable software tools
  • On-line tools and databases

 

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
 Tuller ChimeraUGEM Unsupervised Gene Expression Modeling

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

Borenstein MUSiCC Normalization and correction of microbiome gene abundance profiles
Borenstein FishTaco Quantification of taxonomic drivers of functional microbiome shifts
Borenstein NetSeed Metabolic network-based prediction of biochemical environments 
Borenstein NetCooperate Prediction of host-microbe and microbe-microbe cooperation
Borenstein MIMOSA Identification of drivers of microbiome metabolomic variation 
Borenstein CoMiDA An algorithm for designing simple microbial communities 
Borenstein EMPANADA  Evidence-based, assignment of gene families to pathways in metagenomic data
Borenstein MetaDecon Metagenomic deconvolution 
Pasmanik-Chor HeatMapViewer Interactive display of 2D biological data
Pasmanik-Chor BioNSi Simulation and visualization of multiple KEGG pathways
Pasmanik-Chor GEView Intuitive visualization of expression data

 

 

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