Gitools protocols

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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 in pipelines

 (3)
2017
PMCID: 5363084
PMID: 28333132
DOI: 10.1038/srep44827

[…] of relative gene expression of the salmonella enterica serovar typhimurium sl1344 wild-type and δptsn mutant strains were calculated. the heat map and hierarchical clusters were then generated using gitools v2.2.2., the total rna samples were treated with rnase-free dnase (thermofisher scientific), and cdna was synthesized using rna to cdna ecodrytm premix (random hexamers) (clontech). […]

2014
PMCID: 4109884
PMID: 25058496
DOI: 10.1371/journal.pgen.1004493

[…] data were analyzed using “affy” package and differential expression analysis by “limma” package . functional and pathway enrichment analysis of differentially expressed genes were counducted using gitools . see for detail., we are grateful to t. schüpbach, l-m. pai, a. tyner, and the bloomington stock center for fly stocks and antibodies, and j. o'bryan for pcdna3/ha-c-cbl. we are thankful […]

2014
PMCID: 4252108
PMID: 25460179
DOI: 10.1371/journal.pone.0114491

[…] exact test p values (−log scale) for gene enrichment of each go term in each go group and an enrichment score of >1.3 is considered significant ., somatic mutation data were displayed using gitools (version 1.8.4) . copy number data were displayed using integrative genomics viewer (igv, version 2.3.25) . bee swarm and box plots were created using the beeswarm package in the cran […]


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Gitools in publications

 (66)
PMCID: 5828655
PMID: 29247872
DOI: 10.1016/j.gpb.2017.03.005

[…] that are known to interact with p53 , , , were prepared as a target module . the module was tested to see whether the representative genes were over-represented for functions in this module using gitools with multiple tests corrected p values (fdr) for enrichment. a detail list of these 56 genes is presented in ., note: 56 genes encoding proteins that are known to interact with p53 , , , […]

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

[…] 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., following tmev infection, serum and whole brain or hippocampal homogenates were collected, clarified, and stored at − 80 °c until analysis. mouse ccl2 was detected using […]

PMCID: 5712565
PMID: 29238355
DOI: 10.3389/fpls.2017.02033

[…] using a phosphogluconate-dehydrogenase gene (unigene id: ta30797) for normalization (). the relative expression values (fold change) were converted to log2 values, clustered and visualized with the gitools software (). ranking of genes was defined with the following formula: relative change = abs {average [cheyenne + chinese spring(cheyenne 5a)] - chinese spring}., leaf and crown samples (ca 50 […]

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

[…] 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; […]

PMCID: 5660761
PMID: 29158773
DOI: 10.1155/2017/9426280

[…] zi represents the gene-level statistics of ith gene, and m denotes the count of genes enriched in this given pathway., with the goal of analyzing the changes of pathways in pmop and control samples, gitools [] was utilized to construct the cluster heatmap of pathways. t-test was used to measure the pathway statistics of each pathway in all samples of the two groups. all the premenopause samples […]


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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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