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Gitools specifications

Information


Unique identifier OMICS_03222
Name Gitools
Interface Web user interface
Restrictions to use None
Programming languages Java
Parallelization CUDA
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Núria López-Bigas

Publication for Gitools

Gitools citations

 (29)
library_books

Neuronal CCL2 expression drives inflammatory monocyte infiltration into the brain during acute virus infection

2017
PMCID: 5715496
PMID: 29202854
DOI: 10.1186/s12974-017-1015-2

[…] nome Facility Gene Expression Core. Expression data were analyzed using Excel and MATLAB, where fold change was calculated and converted to log2. Heatmaps and hierarchical clusters were derived using Gitools v2.2.2. […]

library_books

MicroRNAs promote skeletal muscle differentiation of mesodermal iPSC derived progenitors

2017
Nat Commun
PMCID: 5665910
PMID: 29093487
DOI: 10.1038/s41467-017-01359-w

[…] Variance, count and fold change analyses, as well as charts and z.test matrices were conducted by means of Excel software (Microsoft). Heat maps were obtained analyzing the z.test value matrices with GITools 2.2.2 (hierarchical clustering, Manhattan distance, average linkage). Data about 3ʹUTR binding prediction and related mirsvr scores were obtained from microRNA.org, (Aug 2010 release; conserve […]

library_books

Genomic characterization of tobacco/nut chewing HPV negative early stage tongue tumors identify MMP10 as a candidate to predict metastases

2017
Oral Oncol
PMCID: 5628952
PMID: 28939077
DOI: 10.1016/j.oraloncology.2017.08.003

[…] tudies and databases were carried out using previously described method (http://nemates.org/MA/progs/representation.stats.html). The mutual exclusivity and co-occurrence analysis were performed using Gitools . The significant differences between selected two groups were estimated using Unpaired Student t-test and P-value <0.05 was considered as a threshold for statistical significance. […]

library_books

A strategy for the identification of patterns in the biosynthesis of nonribosomal peptides by Betaproteobacteria species

2017
Sci Rep
PMCID: 5583390
PMID: 28871139
DOI: 10.1038/s41598-017-11314-w

[…] The stand-alone software Gitools v.2.2.2 was utilized to provide integrative and visual analyses of POPs and species of the class BPB. The analysis based on the creation of heatmaps using hierarchical methods were carried out […]

library_books

The Correlation between Chemical Structures and Antioxidant, Prooxidant, and Antitrypanosomatid Properties of Flavonoids

2017
PMCID: 5511661
PMID: 28751930
DOI: 10.1155/2017/3789856

[…] The heatmaps were built using the software Gitools 2.3.1 [], based on their biological activities against L. donovani, T. brucei, T. cruzi, and L6 cell toxicity. The data treatment was based on several matrices containing different sets of inf […]

library_books

Genomic analysis of oesophageal squamous cell carcinoma identifies alcohol drinking related mutation signature and genomic alterations

2017
Nat Commun
PMCID: 5477513
PMID: 28548104
DOI: 10.1038/ncomms15290

[…] ated more frequently than expected by chance. To avoid false positive, only regions with FDR q<0.05 and >3% mutation samples were considered significant. Mutual exclusive analysis was performed using gitools (v2.2.2). All statistical analyses were performed in R using standard implementation.We analysed copy number using SynthEx (unpublished, http://chenmengjie.github.io/SynthEx). In brief, 100 kb […]

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Gitools institution(s)
Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, University Pompeu Fabra, Barcelona, Spain

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