Babelomics pipeline

Babelomics specifications

Information


Unique identifier OMICS_00748
Name Babelomics
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 5.0
Stability Stable
Registration required Yes
Maintained Yes

Subtool


  • SNOW

Versioning


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Maintainer


  • person_outline Joaquín Dopazo <>

Information


Unique identifier OMICS_00748
Name Babelomics
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 5.0
Stability Stable
Maintained Yes

Subtool


  • SNOW

Maintainer


  • person_outline Joaquín Dopazo <>

Publications for Babelomics

Babelomics citations

 (4)
2017
PMCID: 5483458

[…] differentially expressed genes respect to a reference group composed of all genes in the microarray with an arabidopsis thaliana homolog was carried out using the program fatigo+ (babelomics, http://babelomics.bioinfo.cipf.es) (ballester et al., 2011). a fisher two-tailed test (p-value < 0.05) was independently performed for gene ontology analysis of induced and repressed genes., special […]

2012
PMCID: 3346234

[…] tm4 microarray software suite (saeed et al., 2003). genes that satisfied a statistical threshold (false discovery rate, fdr) of <0.01 were identified as differentially expressed genes. fatigo+ (babelomics, http://bioinfo.cipf.es/), developed by al-shahrour et al. (2004), was used to identify biological processes significantly under- or over-represented in a particular set of differentially […]

2011
PMCID: 3129315

[…] wing shape in comparison to the control line, for each sex separately, to look for blocks of functionally related genes with similar phenotypic effects across the list. both programmes belong to the babelomics suite of bioinformatic tools which is available online [71]. they both distribute the genes among the terms corresponding to each category in a non-exclusive manner (that is, a given gene […]

2010
PMCID: 2896184

[…] this is a simple but potentially powerful approach to population stratification, which can use the whole genome snp data., this module inherits the functionality of the previous version of babelomics (12,13) although many novelties have been included. apart from the functional enrichment methods such as the popular fatigo (30), and gene set analysis methods such as the segmentation […]

Babelomics institution(s)
Computational Genomics Department, Centro de Investigacio n Principe Felipe (CIPF), Valencia, Spain; Computational Genomics Chair, Bull-CIPF, Valencia, , Spain; Bioinformatics of Rare Diseases (BIER), CIBER de Enfermedades Raras (CIBERER), Valencia, Spain; Department of Medicine, University of Cambridge, School of Clinical Medicine, Addenbrooke’s Hospital, Cambridge, UK; Fundacion Investigacion Clinico de Valencia - INCLIVA, Valencia, Spain; Functional Genomics Node, (INB) at CIPF, Valencia, Spain; HPC Services, University of Cambridge, Cambridge, UK
Babelomics funding source(s)
Supported by Spanish Ministry of Economy and Competitiveness [BIO2011-27069], Conselleria d’Educacio of the Valencian Community [PROMETEOII/2014/025]; EU FP7-PEOPLE Project MLPM [316861]; Fundacio la Marato TV3 [151/C/2013].

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