MetQy – Query Metabolic Functions of Genes and Genomes

MetQy

:: DESCRIPTION

MetQy (metabolic query) is a R package to ease interfacing with the Kyoto Encyclopedia of Genes and Genomes (KEGG) database to query metabolic functions of genes and genomes.

::DEVELOPER

OSS-Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOs
  • R

:: DOWNLOAD

MetQy

:: MORE INFORMATION

Citation

Bioinformatics. 2018 Dec 1;34(23):4134-4137. doi: 10.1093/bioinformatics/bty447.
MetQy-an R package to query metabolic functions of genes and genomes.
Martinez-Vernon AS, Farrell F, Soyer OS

BosFinder – pre-microRNA Gene prediction algorithm in Bos taurus

BosFinder

:: DESCRIPTION

BosFinder is a new algorithm which was developed to identify and annotate the whole genome’s derived pre-miRNAs.

::DEVELOPER

Laboratory of Systems Biology & Bioinformatics (LBB)

:: SCREENSHOTS

BosFinder

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 BosFinder

:: MORE INFORMATION

Citation

Anim Genet. 2014 May 17. doi: 10.1111/age.12170. [Epub ahead of print]
BosFinder: a novell pre-microRNA gene prediction algorithm in Bos taurus.
Sadeghi B1, Ahmadi H, Azimzadeh-Jamalkandi S, Nassiri MR, Masoudi-Nejad A.

NEMO 1.5.2 – Analyzing Gene and Chromosome Territory Distributions from 3D-FISH Experiments

NEMO 1.5.2

:: DESCRIPTION

NEMO is a new Smart 3D-FISH (Three-dimensional fluorescence in situ hybridization) graphical user interface which provides all information in the same place so that results can be checked and validated efficiently.

::DEVELOPER

NEMO team

:: SCREENSHOTS

NEMO

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java
  • ImageJ

:: DOWNLOAD

 NEMO

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Mar 1;26(5):696-7. doi: 10.1093/bioinformatics/btq013. Epub 2010 Jan 14.
NEMO: a tool for analyzing gene and chromosome territory distributions from 3D-FISH experiments.
Iannuccelli E1, Mompart F, Gellin J, Lahbib-Mansais Y, Yerle M, Boudier T.

PsyGeNET v2 / Psygenet2r 1.4.0 – Knowledge Platform on Psychiatric Disorders and their Genes

PsyGeNET v2 / Psygenet2r 1.4.0

:: DESCRIPTION

PsyGeNET (Psychiatric disorders Gene association NETwork) is a resource for the exploratory analysis of psychiatric diseases and their associated genes.

Psygenet2r is an R package for querying PsyGeNET and to perform comorbidity studies in psychiatric disorders

::DEVELOPER

The Integrative Biomedical Informatics group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/windows/MacOsX
  • R

:: DOWNLOAD

Psygenet2r

:: MORE INFORMATION

Citation

Gutiérrez-Sacristán A, Grosdidier S, Valverde O, Torrens M, Bravo À, Piñero J, Sanz F, Furlong LI.
PsyGeNET: a knowledge platform on psychiatric disorders and their genes.
Bioinformatics. 2015 Sep 15;31(18):3075-7. doi: 10.1093/bioinformatics/btv301.

mBISON – Find Enrichment of miRNA Targets on lists of Genes

mBISON

:: DESCRIPTION

mBISON (Analysis on miRNA binding site over-representation) finds over-represented miRNA targets in a gene list you provide.

::DEVELOPER

Computational Biology and Data Mining (CBDM) Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Res Notes. 2015 Apr 16;8:157. doi: 10.1186/s13104-015-1118-8.
mBISON: Finding miRNA target over-representation in gene lists from ChIP-sequencing data.
Gebhardt ML, Mer AS, Andrade-Navarro MA.

 

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PESCADOR – Extract and Analyse a Network of Gene and Protein Interactions from a set of Medline abstracts

PESCADOR

:: DESCRIPTION

PESCADOR (Platform for Exploration of Significant Concepts AssociateD to co-Occurrences Relationships) is a web tool that extracts a network of interactions from a set of PubMed abstracts given by a user, and allows filtering the interaction network according to user-defined concepts.

::DEVELOPER

Computational Biology and Data Mining (CBDM) Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 Nov 9;12:435. doi: 10.1186/1471-2105-12-435.
PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries.
Barbosa-Silva A1, Fontaine JF, Donnard ER, Stussi F, Ortega JM, Andrade-Navarro MA.

CellFinder 1.5.1 – Study Annotations, Bibliography, Gene and Protein Expression in Stem Cells and Derivatives

CellFinder 1.5.1

:: DESCRIPTION

CellFinder maps validated gene and protein expression, phenotype and images related to cell types. The data allow characterization and comparison of cell types and can be browsed by using the body browser and by searching for cells or genes. All cells are related to more complex systems such as tissues, organs and organisms and arranged according to their position in development.

::DEVELOPER

Computational Biology and Data Mining (CBDM) Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2014 Jan;42(Database issue):D950-8. doi: 10.1093/nar/gkt1264. Epub 2013 Dec 3.
CellFinder: a cell data repository.
Stachelscheid H1, Seltmann S, Lekschas F, Fontaine JF, Mah N, Neves M, Andrade-Navarro MA, Leser U, Kurtz A.

Arete 4.0 – An Analysis Toolkit for Network-based Gene Prioritisation

Arete 4.0

:: DESCRIPTION

Arete is an analysis toolkit for network-based gene prioritisation

::DEVELOPER

Laboratory for Medical Science Mathematics

:: SCREENSHOTS

Arete

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • JRE
  • Cytoscape

:: DOWNLOAD

 Arete

:: MORE INFORMATION

Citation

BioData Min. 2017 Jul 6;10:22. doi: 10.1186/s13040-017-0141-9.
Arete – candidate gene prioritization using biological network topology with additional evidence types.
Lysenko A, Boroevich KA, Tsunoda T.

BioGPS – Gene Annotation Portal

BioGPS

:: DESCRIPTION

BioGPS is a centralized gene-annotation portal that enables researchers to access distributed gene annotation resources.

::DEVELOPER

The Su Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

BioGPS: building your own mash-up of gene annotations and expression profiles.
Wu C, Jin X, Tsueng G, Afrasiabi C, Su AI.
Nucleic Acids Res. 2016 Jan 4;44(D1):D313-6. doi: 10.1093/nar/gkv1104

MUFFINN – Cancer Gene Discovery via Network Analysis of Somatic Mutation data

MUFFINN

:: DESCRIPTION

MUFFINN (MUtations For Functional Impact on Network Neighbors) is a method for prioritizing cancer genes accounting for not only for mutations of individual genes but also those of neighbors in functional networks

::DEVELOPER

Network Biomedicine Laboratory at Yonsei University, Korea

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

MUFFINN

:: MORE INFORMATION

Citation

MUFFINN: cancer gene discovery via network analysis of somatic mutation data.
Cho A, Shim JE, Kim E, Supek F, Lehner B, Lee I.
Genome Biol. 2016 Jun 23;17(1):129. doi: 10.1186/s13059-016-0989-x.