Browsing by Document Type "Software"

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  • 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.
  • Furney, Simon J.; Madden, Stephen F.; Kisiel, Tomasz A.; Higgins, Desmond G.; López Bigas, Núria (Universitat Pompeu Fabra, 2007-12)
    Cancer gene properties.
  • Andrzejak, Ralph Gregor; Kreuz, Thomas (2011)
    This source code allows you to calculate the different measures used in: Andrzejak RG, Kreuz T (2011): Characterizing unidirectional couplings between point processes and flows. EPL, 96, 50012.
  • Andrzejak, Ralph Gregor; Mormann, Florian; Kreuz, Thomas (2014)
    In order to understand the source code, you should first read the manuscript (Andrzejak RG, Mormann F, Kreuz T. 2014. Detecting determinism from point processes. Phys. Rev. E. 90, 062906) You will find a Zip-File ...
  • Andrzejak, Ralph Gregor; Ledberg, Anders; Deco, Gustavo (2006)
    This source code allows you to calculate the different measures used in: Andrzejak RG, Ledberg A, Deco G (2006): Detecting event-related time-dependent directional couplings. New Journal of Physics 8, 6. If you use the ...
  • 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
  • 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.
  • Andrzejak, Ralph Gregor; Ruzzene, Giulia; Malvestio, Irene (2017)
    In order to understand the source code, you should first read the manuscript (Andrzejak RG, Ruzzene G, Malvestio I. 2017. Generalized synchronization between chimera states. Chaos. 27(5): 053114). You will find a MATLAB ...
  • 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
  • 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.
  • Leguia, Marc G; Martínez, Cristina G. B.; Malvestio, Irene; Tauste Campo, Adrià; Rocamora, Rodrigo; Levnajić, Zoran; Andrzejak, Ralph Gregor (Universitat Pompeu Fabra, 2019)
    In order to understand the source code of "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. Phys. Rev. E. ...
  • 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.
  • Déu Pons, Jordi (Universitat Pompeu Fabra, 2016-04)
    Python tab files parsing and validating schema tools.
  • Déu Pons, Jordi; Schroeder, Michael Philipp, 1986-; López Bigas, Núria (Universitat Pompeu Fabra, 2014-03)
    Javascript library to create interactive heatmaps within webpages.
  • 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.
  • Andrzejak, Ralph Gregor; Schindler, Kaspar A.; Rummel, Christian (2012)
    Overview: This page provides information about the source code, data, and results provided along with the manuscript [1]. If you use any of these resources, please make sure that you cite reference [1]. This will allow ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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, ...