Browsing by Document Type "Software"

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  • C10-HDAC7
    Barneda Zahonero, Bruna; Román González, Lidia; Collazo, Olga; Rafati, Haleh; Islam, Abul, 1978-; Bussmann, Lars; Di Tullio, Alessandro, 1982-; Andrés, Luisa De; Graf, T. (Thomas); López Bigas, Núria; Mahmoudi, Tokameh; Parra, Maribel (Universitat Pompeu Fabra, 2013-05)
    HDAC7 is a repressor of myeloid genes whose downregulation in pre-B cells is required for transdifferentiation into macrophages.
  • CGProp
    Furney, Simon J.; Madden, Stephen F.; Kisiel, Tomasz A.; Higgins, Desmond G.; López Bigas, Núria (Universitat Pompeu Fabra, 2007-12)
    Cancer gene properties.
  • Characterizing unidirectional couplings between point processes and flows [dataset]
    Andrzejak, Ralph Gregor; Kreuz, Thomas (2011)
    This page provides the source code and results underlying the manuscript: Andrzejak RG, Kreuz T (2011): Characterizing unidirectional couplings between point processes and flows. EPL, 96, 50012 If you use any of these ...
  • Detecting determinism from point processes [software]
    Andrzejak, Ralph Gregor; Mormann, Florian; Kreuz, Thomas (2014)
    This page provides the source code underlying the manuscript: Andrzejak RG, Mormann F, Kreuz T. 2014. Detecting determinism from point processes. Phys. Rev. E. 90, 062906 If you use any of these resources, please make ...
  • Detecting event-related time-dependent directional couplings [software]
    Andrzejak, Ralph Gregor; Ledberg, Anders; Deco, Gustavo (2006)
    This page provides the source code underlying the manuscript: Andrzejak RG, Ledberg A, Deco G (2006): Detecting event-related time-dependent directional couplings. New Journal of Physics 8, 6 If you use any of these ...
  • Evolvavility
    López Bigas, Núria; De, Subhajyoti; Teichmann, Sarah A. (Universitat Pompeu Fabra, 2007-10)
    Mutations, genes and pathways involved in tumorigenesis across 4,623 cancer genomes/exomes from 13 cancer sites. IntOGen-mutations identifies cancer drivers across tumor types. Nature Methods 10, 2013, doi:10.1038/nmeth.2642
  • funcSTAR
    Shikhagaie, Medya; López Bigas, Núria (Universitat Pompeu Fabra, 2007-10)
    Web tool for the selection of SNPs from the STAR project with potential functional effect.
  • Generalized synchronization between chimera states [software]
    Andrzejak, Ralph Gregor; Ruzzene, Giulia; Malvestio, Irene (2017)
    This page provides the source code underlying the manuscript: Andrzejak RG, Ruzzene G, Malvestio I. 2017. Generalized synchronization between chimera states. Chaos. 27(5): 053114 If you use any of these resources, please ...
  • Gitools
    Pérez Llamas, Christian, 1976-; López Bigas, Núria; Schroeder, Michael Philipp, 1986-; Déu Pons, Jordi (Universitat Pompeu Fabra, 2016-07-05)
    Gitools is a framework for analysis and visualization of multidimensional genomic data using interactive heat-maps
  • iDGP
    Furney, Simon J.; Albà Soler, Mar; López Bigas, Núria (Universitat Pompeu Fabra, 2006-07)
    Database of human genes prioritized for their probability of involvement in dominant or recessive hereditary diseases.
  • Inferring directed networks using a rank-based connectivity measure [software]
    Leguia, Marc G.; Martínez, Cristina G. B.; Malvestio, Irene; Tauste Campo, Adrià; Rocamora, Rodrigo; Levnajić, Zoran; Andrzejak, Ralph Gregor (Universitat Pompeu Fabra, 2019)
    This page provides the source code underlying the manuscript: Leguia MG, Martínez CGB, Malvestio I, Campo A T, Rocamora R, Levnajic Z, Andrzejak RG. 2019. Inferring directed networks using a rank-based connectivity measure. ...
  • IntOGen - Pipeline
    González-Pérez, Abel; Pérez Llamas, Christian, 1976-; Tamborero Noguera, David; Schroeder, Michael Philipp, 1986-; Jené i Sanz, Alba, 1984-; Santos, Alberto; López Bigas, Núria; Déu Pons, Jordi (Universitat Pompeu Fabra, 2016-07-18)
    Analyses somatic mutations in thousands of tumor genomes to identify cancer driver genes.
  • itab
    Déu Pons, Jordi (Universitat Pompeu Fabra, 2016-04)
    Python tab files parsing and validating schema tools.
  • jHeatmap
    Déu Pons, Jordi; Schroeder, Michael Philipp, 1986-; López Bigas, Núria (Universitat Pompeu Fabra, 2014-03)
    Javascript library to create interactive heatmaps within webpages.
  • Mutations Needle Plot (muts-needle-plot)
    Schroeder, Michael Philipp, 1986- (Universitat Pompeu Fabra, 2015-11)
    A needle-plot (aka stem-plot or lollipop-plot) plots each data point as a big dot and adds a vertical line that makes it appear like a needle.
  • Nonrandomness, nonlinear dependence, and nonstationarity of electroencephalographic recordings from epilepsy patients [dataset]
    Andrzejak, Ralph Gregor; Schindler, Kaspar A.; Rummel, Christian (2012)
    This page provides the source code, data, and detailed results of the manuscript: Andrzejak RG, Schindler K, Rummel C. Nonrandomness, nonlinear dependence, and nonstationarity of electroencephalographic recordings from ...
  • Oncodrive-CIS
    Tamborero Noguera, David; López Bigas, Núria; González-Pérez, Abel (Universitat Pompeu Fabra, 2013-02)
    Oncodrive-CIS is a method aimed to identify those copy number alterations (CNAs) leading to larger in cis expression changes that may be useful in elucidating the role of these aberrations in cancer. This is based on the ...
  • OncodriveCLUST
    Tamborero Noguera, David; González-Pérez, Abel; López Bigas, Núria (Universitat Pompeu Fabra, 2015-11)
    OncodriveCLUST is a method aimed to identify genes whose mutations are biased towards a large spatial clustering. This method is designed to exploit the feature that mutations in cancer genes, especially oncogenes, often ...
  • OncodriveFM
    González-Pérez, Abel; López Bigas, Núria (Universitat Pompeu Fabra, 2015-10)
    OncodriveFM detects candidate cancer driver genes and pathways from catalogs of somatic mutations in a cohort of tumors by computing the bias towards the accumulation of functional mutations (FM bias).This novel approach ...
  • OncodriveFML
    Mularoni, Loris; Sabarinathan, Radhakrishnan; González-Pérez, Abel; López Bigas, Núria; Déu Pons, Jordi (Universitat Pompeu Fabra, 2016-06-06)
    Method to identify genomic regions, both coding and non-coding, bearing mutations with significant shift towards high functional impact across a cohort of tumos (FMbias), which are candidates to function as cancer drivers, ...