IntervalStats – Statistical Evaluation of ChIPseq Dataset Similarity

IntervalStats

:: DESCRIPTION

IntervalStats is an effective statistical evaluation of ChIPseq dataset similarity.

::DEVELOPER

Chikina Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 IntervalStats

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Mar 1;28(5):607-13. doi: 10.1093/bioinformatics/bts009.
An effective statistical evaluation of ChIPseq dataset similarity.
Chikina MD, Troyanskaya OG.

SPELL 2.0.3 – Serial Pattern of Expression Levels Locator

SPELL 2.0.3

:: DESCRIPTION

SPELL is a query-driven search engine for large gene expression microarray compendia. Given a small set of query genes, SPELL identifies which datasets are most informative for these genes, then within those datasets additional genes are identified with expression profiles most similar to the query set.

::DEVELOPER

Troyanskaya Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2007 Oct 15;23(20):2692-9.
Exploring the functional landscape of gene expression: directed search of large microarray compendia.
Hibbs MA, Hess DC, Myers CL, Huttenhower C, Li K, Troyanskaya OG.

IMP 2.0 – Integrative Multi-species Prediction

IMP 2.0

:: DESCRIPTION

IMP is an interactive web server that enables molecular biologists to interpret experimental results and to generate hypotheses in the context of a large cross-organism compendium of functional predictions and networks.

::DEVELOPER

Troyanskaya Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Wong AK*, Krishnan A*, Yao V*, Tadych A, Troyanskaya OG.
IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks.
Nucleic Acids Research. July 2015;43:W128-W133.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W484-90. doi: 10.1093/nar/gks458.
IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks.
Wong AK, Park CY, Greene CS, Bongo LA, Guan Y, Troyanskaya OG.

AMBER 20 – Assisted Model Building with Energy Refinement

AMBER 20

:: DESCRIPTION

AMBER (Assisted Model Building with Energy Refinement) refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.

::DEVELOPER

AMBER Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  MacOsX / Window with Cygwin
  • Fortran 95, C and C++ compilers.

:: DOWNLOAD

AMBER

:: MORE INFORMATION

Citation

D.A. Case, T.E. Cheatham, III, T. Darden, H. Gohlke, R. Luo, K.M. Merz, Jr., A. Onufriev, C. Simmerling, B. Wang and R. Woods. The Amber biomolecular simulation programsJ. Computat. Chem.26, 1668-1688 (2005).

NNN 1.01 – Nearest Neighbor Networks Clustering

NNN 1.01

:: DESCRIPTION

NNN (Nearest Neighbor Networks) is a graph-based algorithm to generate clusters of genes with similar expression profiles. This method produces clusters based on overlapping cliques within an interaction network generated from mutual nearest neighborhoods. This focus on nearest neighbors rather than on absolute distance measures allows us to capture clusters with high connectivity even when they are spatially separated, and requiring mutual nearest neighbors allows genes with no sufficiently similar partners to remain unclustered. We compared the clusters generated by NNN with those generated by eight other clustering methods. NNN was particularly successful at generating functionally coherent clusters with high precision, and these clusters generally represented a much broader selection of biological processes than those recovered by other methods.

::DEVELOPER

NNN team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • java

:: DOWNLOAD

 NNN

:: MORE INFORMATION

Citation

Huttenhower, C., Flamholz, A., Landis, J., Sahi, S., Myers, C., Olszewski, K., Hibbs, M., Siemers, N., Troyanskaya, O., Coller, H.,
Nearest Neighbor Networks: Clustering Expression Data Based on Gene Neighborhoods“,
BMC Bioinformatics 8:250, 2007

Sleipnir 3.0 / COALESCE – Library for Computational Functional Genomics

Sleipnir 3.0 / COALESCE

:: DESCRIPTION

Sleipnir is a C++ library enabling efficient analysis, integration, mining, and machine learning over genomic data. This includes a particular focus on microarrays, since they make up the bulk of available data for many organisms, but Sleipnir can also integrate a wide variety of other data types, from pairwise physical interactions to sequence similarity or shared transcription factor binding sites.

COALESCE (Combinatorial Algorithm for Expression and Sequence-based Cluster Extraction) can use large collections of genomic data and Bayesian integration to predict coregulated gene modules, the conditions of regulation, and the consensus binding motifs for regulation.

::DEVELOPER

Troyanskaya Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • C Compiler

:: DOWNLOAD

 Sleipnir

:: MORE INFORMATION

Citation

Curtis Huttenhower, Mark Schroeder, Maria D. Chikina, and Olga G. Troyanskaya
The Sleipnir library for computational functional genomics”,
Bioinformatics. 2008 Jul 1;24(13):1559-61. Epub 2008 May 21.

Bioinformatics. 2009 Dec 15;25(24):3267-74. doi: 10.1093/bioinformatics/btp588.
Detailing regulatory networks through large scale data integration.
Huttenhower C, Mutungu KT, Indik N, Yang W, Schroeder M, Forman JJ, Troyanskaya OG, Coller HA.

JustClust – Analysing Biological Data with Cluster Analysis

JustClust

:: DESCRIPTION

JustClust is a tool for analysing biological data with cluster analysis. JustClust can handle many formats of data and cluster the data with many state-of-the-art techniques. The aim of JustClust is to provide an easy-to-use application which can perform any analysis on any data.

::DEVELOPER

Paccanaro Lab

:: SCREENSHOTS

::REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 JustClust

:: MORE INFORMATION

GOssTo 1.01 – the Gene Ontology Semantic Similarity Tool

GOssTo 1.01

:: DESCRIPTION

GOssTo is a Java based semantic similarity calculator. Bundled in the software are the well-known Resnik, Lin, Jian, simUI, simGRASM similarity measures. It features powerful extension capabilities allowing the user to add as many similarity measures as needed.

::DEVELOPER

Paccanaro Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

  GOssTo

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 22. [Epub ahead of print]
GOssTo: a user-friendly stand-alone and web tool for calculating semantic similarities on the Gene Ontology.
Caniza H1, Romero AE, Heron S, Yang H, Devoto A, Frasca M, Mesiti M, Valentini G, Paccanaro A.

RefLnc – comprehensive Annotation for human long noncoding RNAs(lncRNAs)

RefLnc

:: DESCRIPTION

RefLnc is a comprehensive annotation for human long noncoding RNAs(lncRNAs).Each lncRNA in the atlas is characterized by a panorama of sequence, expression and trait association.

::DEVELOPER

Gao Lab, Peking University.

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • R

:: DOWNLOAD

RefLnc

:: MORE INFORMATION

Citation

Jiang S, Cheng SJ, Ren LC, Wang Q, Kang YJ, Ding Y, Hou M, Yang XX, Lin Y, Liang N, Gao G.
An expanded landscape of human long noncoding RNA.
Nucleic Acids Res. 2019 Sep 5;47(15):7842-7856. doi: 10.1093/nar/gkz621. PMID: 31350901; PMCID: PMC6735957.