{"id":2499,"date":"2017-02-28T08:49:26","date_gmt":"2017-02-28T08:49:26","guid":{"rendered":"http:\/\/acgt.cs.tau.ac.il\/?page_id=2499"},"modified":"2024-09-11T07:20:12","modified_gmt":"2024-09-11T07:20:12","slug":"software","status":"publish","type":"page","link":"https:\/\/acgt.cs.tau.ac.il\/?page_id=2499","title":{"rendered":"Software"},"content":{"rendered":"

Software tools and Projects<\/h1>\n

Add new software<\/a><\/p>\n\n\n\n

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Integrating mutation, copy number, and gene expression data to identify driver genes of recurrent chromosome-arm losses<\/p>\n\n <\/div>\n

\n \"\"\n
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Aneuploidy Drivers<\/div>\n \t
<\/div>\n \tAneuploidy Drivers homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n\t\t\n\t\t\n\t\t\t
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A data-driven method to optimize the clinical scales for Parkinson\u2019s disease, improving its ability to track disease progression.<\/p>\n\n <\/div>\n

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MOPS<\/div>\n \t
<\/div>\n \tMOPS homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n \t\t\n\t\t\n\t\t\t
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A novel two-stage clinical trial design that meets regulatory requirements while enhancing real-world outcomes and fairness.<\/p>\n\n <\/div>\n

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RFAN<\/div>\n \t
<\/div>\n \tRFAN homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n\t\t\n\t\t\n\t\t\t
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4-class classifier of metagenome contigs using machine learning and assembly graphs<\/p>\n\n <\/div>\n

\n \"\"\n
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4CAC<\/div>\n \t
<\/div>\n \t4CAC homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t
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Integrating gene expression and DNA methylation datasets for disjoint sample sets.<\/p>\n\n <\/div>\n

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Intend<\/div>\n \t
<\/div>\n \tIntend homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n\t\t\n\t\t\n\t\t\t
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Selecting minimizers based on minimum decycling set.<\/p>\n\n <\/div>\n

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MDS Minimizers<\/div>\n \t
<\/div>\n \tMDS Minimizers homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n \t\t\n\t\t\n\t\t\t
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CT-FOCS - A database of cell type-specific enhancer-promoter links<\/p>\n\n <\/div>\n

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CT-FOCS <\/div>\n \t
<\/div>\n \tCT-FOCS homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n\t\t\n\t\t\n\t\t\t
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Long-read mapping using syncmers.<\/p>\n\n <\/div>\n

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Syncmer Mapping<\/div>\n \t
<\/div>\n \tSyncmer Mapping homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t
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Accurate module discovery using gene activities and a network<\/p>\n\n <\/div>\n

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DOMINO<\/div>\n \t
<\/div>\n \tDOMINO homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n\t\t\n\t\t\n\t\t\t
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Dataset adaptive minimizer order generator for binning applications<\/p>\n\n <\/div>\n

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AdaOrder and DGerbil<\/div>\n \t
<\/div>\n \tAdaOrder and DGerbil homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n \t\t\n\t\t\n\t\t\t
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3-class classification of metagenome assemblies<\/p>\n\n <\/div>\n

\n \"\"\n
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3CAC<\/div>\n \t
<\/div>\n \t3CAC homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n\t\t\n\t\t\n\t\t\t
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Multi Omic clustering by Non-Exhaustive Types<\/p>\n\n <\/div>\n

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MONET<\/div>\n \t
<\/div>\n \tMONET homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t
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Complete plasmid assembly in metagenomes<\/p>\n\n <\/div>\n

\n \"\"\n
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SCAPP <\/div>\n \t
<\/div>\n \tSCAPP homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n\t\t\n\t\t\n\t\t\t
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Empirically correcting the functional significance of GO terms in modules<\/p>\n\n <\/div>\n

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EMP<\/div>\n \t
<\/div>\n \tEMP homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n \t\t\n\t\t\n\t\t\t
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PlasClass - Plasmid sequence classifier<\/p>\n\n <\/div>\n

\n \"\"\n
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PlasClass<\/div>\n \t
<\/div>\n \tPlasClass homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n\t\t\n\t\t\n\t\t\t
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EXPANDER - A one stop-shop platform for all analysis steps of gene expression data.<\/p>\n\n <\/div>\n

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Expander<\/div>\n \t
<\/div>\n \tExpander homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t
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PROMO - a tool for analysis and visualization of large multi-omic and clinical datasets.<\/p>\n\n <\/div>\n

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PROMO<\/div>\n \t
<\/div>\n \tPROMO homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n\t\t\n\t\t\n\t\t\t
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NEMO: Neighborhood based multi-omics clustering algorithm<\/p>\n\n <\/div>\n

\n \"\"\n
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Nemo <\/div>\n \t
<\/div>\n \tNemo homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n \t\t\n\t\t\n\t\t\t
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Adeptus - A database and tools for multi-disease analysis.<\/p>\n\n <\/div>\n

\n \"\"\n
\n \t
Adeptus<\/div>\n \t
<\/div>\n \tAdeptus homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n\t\t\n\t\t\n\t\t\t
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Faucet: streaming de novo assembly graph construction<\/p>\n\n <\/div>\n

\n \"\"\n
\n \t
Faucet<\/div>\n \t
<\/div>\n \tFaucet homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t
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FOCS: A database of human and mouse enhancer-promoter links<\/p>\n\n <\/div>\n

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FOCS<\/div>\n \t
<\/div>\n \tFOCS homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n\t\t\n\t\t\n\t\t\t
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Recycler - detecting plasmids from de novo assembly graphs<\/p>\n\n <\/div>\n

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recycler<\/div>\n \t
<\/div>\n \trecycler homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n \t\t\n\t\t\n\t\t\t
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DOCKS - A software for designing \u00a0compact universal k-mers hitting set.<\/p>\n\n <\/div>\n

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Docks<\/div>\n \t
<\/div>\n \tDocks homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n\t\t\n\t\t\n\t\t\t
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RichMind - Analysis of enrichment within neuroimaging findings<\/p>\n\n <\/div>\n

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RichMind<\/div>\n \t
<\/div>\n \tRichMind homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t
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Motif finding from high-throughput SELEX<\/p>\n\n <\/div>\n

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HTS-IBIS<\/div>\n \t
<\/div>\n \tHTS-IBIS homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n\t\t\n\t\t\n\t\t\t
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ElemeNT - Tool for detection of core promoter elements.<\/p>\n\n <\/div>\n

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ElemeNT<\/div>\n \t
<\/div>\n \tElemeNT homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n \t\t\n\t\t\n\t\t\t
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BARCODE - A fast lossless read compression tool based on Bloom filters.<\/p>\n\n <\/div>\n

\n \"\"\n
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barcode<\/div>\n \t
<\/div>\n \tbarcode homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n\t\t\n\t\t\n\t\t\t
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RAP - A software for inferring binding site motifs from protein binding microarrays.<\/p>\n\n <\/div>\n

\n \"\"\n
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RAP<\/div>\n \t
<\/div>\n \tRAP homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t
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HiDe - A software for inferring highways of horizontal gene transfer.<\/p>\n\n <\/div>\n

\n \"\"\n
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HiDe<\/div>\n \t
<\/div>\n \tHiDe homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n\t\t\n\t\t\n\t\t\t
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ShortCAKE - Designing a shortest DNA sequence that covers all k-mers, exploiting reverse complementarity.<\/p>\n\n <\/div>\n

\n \"\"\n
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ShortCake<\/div>\n \t
<\/div>\n \tShortCake homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n \t\t\n\t\t\n\t\t\t
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AMADEUS - Platform for de novo motif discovery in DNA sequences.<\/p>\n\n <\/div>\n

\n \"\"\n
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Amadeus<\/div>\n \t
<\/div>\n \tAmadeus homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n\t\t\n\t\t\n\t\t\t
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Morph - A webtool and software for ranking candidate genes in pathways.<\/p>\n\n <\/div>\n

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Morph<\/div>\n \t
<\/div>\n \tMorph homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t
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ALLEGRO - Software for simultaneous discovery of cis-regulatory motifs and their associated expression profiles.<\/p>\n\n <\/div>\n

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Allegro<\/div>\n \t
<\/div>\n \tAllegro homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n\t\t\n\t\t\n\t\t\t
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ModEnt - A tool that reconstructs gene regulatory networks from high throughput experimental data.<\/p>\n\n <\/div>\n

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ModEnt<\/div>\n \t
<\/div>\n \tModEnt homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n \t\t\n\t\t\n\t\t\t
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STACK - Analyzing statistical associations among cancer karyotypes.<\/p>\n\n <\/div>\n

\n \"\"\n
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Stack<\/div>\n \t
<\/div>\n \tStack homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n\t\t\n\t\t\n\t\t\t
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FAME - A tool for Functional Assignment to MicroRNAs via Enrichment<\/p>\n\n <\/div>\n

\n \"\"\n
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Fame<\/div>\n \t
<\/div>\n \tFame homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t
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TORQUE - Topology-free querying of protein interaction networks.<\/p>\n\n <\/div>\n

\n \"\"\n
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Torque<\/div>\n \t
<\/div>\n \tTorque homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n\t\t\n\t\t\n\t\t\t
\n

MetaReg - A tool for modeling of biological systems<\/p>\n\n <\/div>\n

\n \"\"\n
\n \t
MetaReg<\/div>\n \t
<\/div>\n \tMetaReg homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n \t\t\n\t\t\n\t\t\t
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HYDEN - A software for designing degenerate primers.<\/p>\n\n <\/div>\n

\n \"\"\n
\n \t
HYDEN<\/div>\n \t
<\/div>\n \tHYDEN homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n\t\t\n\t\t\n\t\t\t
\n

SPIKE - (previously SHARP). Signaling pathways integrated knowledge engine.<\/p>\n\n <\/div>\n

\n \"\"\n
\n \t
Spike<\/div>\n \t
<\/div>\n \tSpike homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t
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GEVALT - An integrated software for genotype analysis.<\/p>\n\n <\/div>\n

\n \"\"\n
\n \t
Gevalt<\/div>\n \t
<\/div>\n \tGevalt homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n\t\t\n\t\t\n\t\t\t
\n

PSAT - Evaluating the significance of association scores in whole-genome cohorts with stratification.<\/p>\n\n <\/div>\n

\n \"\"\n
\n \t
Psat<\/div>\n \t
<\/div>\n \tPsat homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n \t\t\n\t\t\n\t\t\t
\n

Cofactors - Linking transcription factors and chromatin modifiers.<\/p>\n\n <\/div>\n

\n \"\"\n
\n \t
cofactors<\/div>\n \t
<\/div>\n \tcofactors homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n\t\t\n\t\t\n\t\t\t
\n

MATISSE - A tool for joint analysis of interaction networks and gene expression data.<\/p>\n\n <\/div>\n

\n \"\"\n
\n \t
Matisse<\/div>\n \t
<\/div>\n \tMatisse homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t
\n\t\t\t
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RAT - A software for rapid association tests.<\/p>\n\n <\/div>\n

\n \"\"\n
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Rat<\/div>\n \t
<\/div>\n \tRat homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n\t\t\n\t\t\n\t\t\t
\n

Cisprof - Evolutionary mechanisms underlying conservation and evolvability in regulatory networks.<\/p>\n\n <\/div>\n

\n \"\"\n
\n \t
Cisprof<\/div>\n \t
<\/div>\n \tCisprof homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n \t\t\n\t\t\n\t\t\t
\n

SIMBA - \u00a0System level analysis of yeast by exploring of large-scale biological compendia.<\/p>\n\n <\/div>\n

\n \"\"\n
\n \t
SIMBA<\/div>\n \t
<\/div>\n \tSIMBA homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n\t\t\n\t\t\n\t\t\t
\n

SAMBA - Module discovery in highly diverse genome-wide datasets using biclustering.<\/p>\n\n <\/div>\n

\n \"\"\n
\n \t
Samba<\/div>\n \t
<\/div>\n \tSamba homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t
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\n

GREAL - software for the graph realization Problem.<\/p>\n\n <\/div>\n

\n \"\"\n
\n \t
GREAL<\/div>\n \t
<\/div>\n \tGREAL homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n\t\t\n\t\t\n\t\t\t
\n

PREVO - An analysis of the network of selection forces in the evolution of yeast cis-regulation<\/p>\n\n <\/div>\n

\n \"\"\n
\n \t
PREVO<\/div>\n \t
<\/div>\n \tPREVO homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n \t\t\n\t\t\n\t\t\t
\n

PRIMA - A program for finding transcription factors whose binding sites are enriched in a given set of promoters.<\/p>\n\n <\/div>\n

\n \"\"\n
\n \t
Prima<\/div>\n \t
<\/div>\n \tPrima homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n\t\t\n\t\t\n\t\t\t
\n

PIVOT - Java-based protein interactions visualization tool.<\/p>\n\n <\/div>\n

\n \"\"\n
\n \t
PIVOT<\/div>\n \t
<\/div>\n \tPIVOT homepage<\/a>\n <\/div>\n <\/div>\n <\/div><\/div>\n\t\t<\/div>\n\t\t\n\t\n\t\n\t\n<\/div>\n\n

The following software tools were phased out. Individuals wishing to use any of them should contact Ron Shamir.<\/h3>\n

Cezanne (Bioinformatics 2009<\/a>)
\n<\/strong>ReL (PLoS Genetics 2010<\/a>)<\/strong>
\n<\/strong>Degas (PLoS One 2010<\/a>)
\n<\/strong>Pmemap (Nat Struc Mol Bio 2011<\/a>)
\nDICER (PLOS Computational Biology 2013)<\/a>
\nModMap (Nucleic Acids Research 2014<\/a>)
\nTWIGS (Bioinformatics 2015<\/a>)<\/strong><\/h3>\n","protected":false},"excerpt":{"rendered":"

Software tools and Projects Add new software The following software tools were phased out. Individuals wishing to use any of them should contact Ron Shamir. Cezanne (Bioinformatics 2009) ReL (PLoS Genetics 2010) Degas (PLoS One 2010) Pmemap (Nat Struc Mol Bio 2011) DICER (PLOS Computational Biology 2013) ModMap (Nucleic Acids Research 2014) TWIGS (Bioinformatics 2015)<\/p>\n","protected":false},"author":9,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"_links":{"self":[{"href":"https:\/\/acgt.cs.tau.ac.il\/index.php?rest_route=\/wp\/v2\/pages\/2499"}],"collection":[{"href":"https:\/\/acgt.cs.tau.ac.il\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/acgt.cs.tau.ac.il\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/acgt.cs.tau.ac.il\/index.php?rest_route=\/wp\/v2\/users\/9"}],"replies":[{"embeddable":true,"href":"https:\/\/acgt.cs.tau.ac.il\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=2499"}],"version-history":[{"count":12,"href":"https:\/\/acgt.cs.tau.ac.il\/index.php?rest_route=\/wp\/v2\/pages\/2499\/revisions"}],"predecessor-version":[{"id":5579,"href":"https:\/\/acgt.cs.tau.ac.il\/index.php?rest_route=\/wp\/v2\/pages\/2499\/revisions\/5579"}],"wp:attachment":[{"href":"https:\/\/acgt.cs.tau.ac.il\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2499"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}