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203 Research products, page 1 of 21

  • Research software
  • 2013-2022
  • Open Source
  • European Commission

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  • Research software . 2022
    Open Source C++
    Authors: 
    Muntoni, Anna Paola;
    Publisher: bio.tools
    Project: EC | INFERNET (734439)

    Adaptive Boltzmann machine learning for Potts models of biological data (adabmDCA) This is an implementation of the Boltzmann machine learning to infer several maximum-entropy statistical models of Potts or Ising variables given a set of observables. More precisely, it infers the couplings and the fields of a set of generalized Direct Coupling Analysis (DCA) models given a Multiple Sequence Alignment (MSA) of protein or RNA sequences. It is also possible to infer an Ising model from a set of spin configurations. The learning is performed via a gradient ascent of the likelihood of the data in which the model observables are computed via a Markov Chain Monte Carlo (MCMC) sampling.

  • Research software . 2022
    Open Source Python
    Authors: 
    Chennen, Kirsley; Weber, Thomas; Poch, Olivier;
    Publisher: bio.tools
    Project: EC | ELIXIR-EXCELERATE (676559), ANR | IFB (ex Renabi-IFB) (ANR-11-INBS-0013)

    MISTIC (MISsense deleTeriousness predICtor), a prediction tool to reveal disease-relevant deleterious missense variants based on an original combination of two complementary machine learning algorithms using a soft voting system that integrates 113 missense features, ranging from multi-ethnic minor allele frequencies and evolutionary conservation, to physiochemical and biochemical properties of amino acids.

  • Research software . 2022
    Open Source C
    Authors: 
    Söding, Johannes;
    Publisher: bio.tools
    Project: EC | Virus-X (685778)

    HH-suite is a remote protein homology detection suite.

  • Research software . 2022
    Open Source R
    Authors: 
    Dopazo, Joaquin;
    Publisher: bio.tools
    Project: EC | ELIXIR-EXCELERATE (676559)

    MIGNON (Mechanistic InteGrative aNalysis Of rNa-seq data) is a versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways.

  • Research software . 2022
    Open Source Python
    Authors: 
    Liedl, Klaus R.;
    Publisher: bio.tools
    Project: EC | NANOSTEM (764958)

    X-Entropy is a parallelized kernel density estimator with automated bandwidth selection to calculate entropy. This library is primarily meant to calculate dihedral entropies from MD simulation data. For this, we use a KDE with automatic bandwidth selection as suggested by Z. Botev et al. We tried to keep the package as generalized as possible, therefore, the package can be used to calculate the entropy of any data, or also to simply calculate the KDE.

  • Research software . 2021
    Open Source Python
    Authors: 
    Fabritiis, Gianni De;
    Publisher: bio.tools
    Project: EC | CompBioMed2 (823712), EC | ScaleCell (772230)

    TorchMD is a deep learning framework for molecular simulations.

  • Research software . 2021
    Open Source R
    Authors: 
    Jokinen, Emmi; Lähdesmäki, Harri;
    Publisher: bio.tools
    Project: EC | M-Imm (647355)

    TCRGP is a novel Gaussian process method that can predict if TCRs recognize certain epitopes. This method can utilize different CDR sequences from both TCRα and TCRβ chains from single-cell data and learn which CDRs are important in recognizing the different epitopes.

  • Research software . 2021
    Open Source Python
    Authors: 
    Mahfouz, Ahmed;
    Publisher: bio.tools
    Project: EC | PAVE (861190)

    scHPL is a hierarchical progressive learning method which automatically finds relationships between cell populations across multiple datasets and uses this to construct a hierarchical classification tree. For each node in the tree either a linear SVM or one-class SVM, which enables the detection of unknown populations, is trained. The trained classification tree can be used to predict the labels of a new unlabeled dataset.

  • Research software . 2021
    Open Source C++
    Authors: 
    Herz, Kai;
    Publisher: bio.tools
    Project: EC | OncoViroMRI (836752)

    Pulseq-CEST is a tool to ensure multi-site multi-vendor compatibility and reproducibility of CEST experiments using an open-source sequence standard.

  • Research software . 2021
    Open Source Groovy
    Authors: 
    Fellows Yates, James A.;
    Publisher: bio.tools
    Project: EC | FoodTransforms (678901)

    A fully reproducible and state-of-the-art ancient DNA analysis pipeline

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