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integration_instructions Research softwarekeyboard_double_arrow_right Software 2021 PythonPublisher:bio.tools Funded by:NWO | BRAINSCAPES: A Roadmap fr..., EC | PAVENWO| BRAINSCAPES: A Roadmap from Neurogenetics to Neurobiology ,EC| PAVEAuthors: Mahfouz, Ahmed;Mahfouz, Ahmed;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.
All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=__bioTools__::4aff7ea6a8a9fd32589c04e536a13908&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=__bioTools__::4aff7ea6a8a9fd32589c04e536a13908&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2019 C++Publisher:bio.tools Funded by:NIH | Microconnectomics of neoc..., WT | Sharing standardised expe..., NIH | Dissemination of a tool f... +6 projectsNIH| Microconnectomics of neocortex: a multiscale computer model ,WT| Sharing standardised experimental data and models of neural systems through the Open Source Brain repository ,NIH| Dissemination of a tool for data-driven multiscale modeling of brain circuits ,NIH| Dissemination of a tool for data-driven multiscale modeling of brain circuits ,NIH| Cortical and thalamic mechanisms of selective auditory attention ,EC| HBP SGA2 ,NIH| Embedded Ensemble Encoding ,WT| The Open Source Brain repository: enabling the collaborative development of open and accessible models for neuroscience ,NIH| Towards a Complete Description of the Circuitry Underlying Sharp Wave-Mediated Memory ReplayAuthors: Arkhipov, Anton;Arkhipov, Anton;Scalable Open Network Architecture TemplAte (SONATA) Data Format for Efficient Description of Large-Scale Network Models.
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For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=__bioTools__::a7c46e02d3db6f8c8648884fc5d9e6b4&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2019Publisher:bio.tools Funded by:EC | HBP SGA2, EC | HBP SGA1EC| HBP SGA2 ,EC| HBP SGA1Authors: Bjaalie, Jan G.; Laboratory, Neural Systems;Bjaalie, Jan G.; Laboratory, Neural Systems;Tool for user guided affine registration (anchoring) of 2D experimental image data, typically high resolution microscopic images, to 3D atlas reference space, facilitating data integration through standardized coordinate systems.
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For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=__bioTools__::4bd00afcbf99211e0368956bd3d48cca&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2019 RPublisher:bio.tools Funded by:EC | SYSCIDEC| SYSCIDAuthors: Yang, Wentao; Schulenburg, Hinrich;Yang, Wentao; Schulenburg, Hinrich;Using polynomial uncertainty modelling for differential gene expression estimation from RNA sequencing data.
All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=__bioTools__::0790acd95b029fec3879ef27df40b906&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=__bioTools__::0790acd95b029fec3879ef27df40b906&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2018 PythonPublisher:bio.tools Funded by:EC | RobustSynapses, EC | cis-CONTROLEC| RobustSynapses ,EC| cis-CONTROLAuthors: Davie, Kristofer; Waegeneer, Maxime De; Kreft, Lukasz;Davie, Kristofer; Waegeneer, Maxime De; Kreft, Lukasz;SCope is a fast visualization tool for large-scale and high dimensional scRNA-seq datasets. Currently the data format supported by SCope is .loom. This file format for very large omics datasets is maintained by the Linnarsson Lab through the loompy Python package (https://github.com/linnarsson-lab/loompy).
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For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=__bioTools__::ab10c610cf1ae816f52b6790b1e65d68&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2015 JavaPublisher:bio.tools Funded by:UKRI | Ensembl and enabling gene..., EC | HELIX NEBULA, WT +10 projectsUKRI| Ensembl and enabling genetics and genomics research in farmed animal species ,EC| HELIX NEBULA ,WT ,WT| Ensembl: current, complete and consistent annotation of large scale genome sequence ,NIH| GENCODE: comprehensive gene annotation for human and mouse ,EC| EURATRANS ,WT| Ensembl ,EC| QUANTOMICS ,NIH| Functional analysis of the zebrafish genome through RNA-seq and ribosome profile ,EC| BLUEPRINT ,UKRI| Ensembl and enabling genetics and genomics research in farmed animal species ,UKRI| Improving the rat reference genome annotation and building community engagement ,EC| SLINGAuthors: Flicek, Paul;Flicek, Paul;Genome databases for vertebrates genomes.
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For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=__bioTools__::cce9821dde6e5879dde269c0202e769b&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2015Publisher:bio.tools Funded by:EC | SISYPHE, EC | ALMONDEC| SISYPHE ,EC| ALMONDAuthors: Chikhi, Rayan; Rizk, Guillaume;Chikhi, Rayan; Rizk, Guillaume;Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.
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For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=__bioTools__::9c6366d5da24b30d7dca6e0b3b5f1ceb&type=result"></script>'); --> </script>
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integration_instructions Research softwarekeyboard_double_arrow_right Software 2021 PythonPublisher:bio.tools Funded by:NWO | BRAINSCAPES: A Roadmap fr..., EC | PAVENWO| BRAINSCAPES: A Roadmap from Neurogenetics to Neurobiology ,EC| PAVEAuthors: Mahfouz, Ahmed;Mahfouz, Ahmed;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.
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For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=__bioTools__::4aff7ea6a8a9fd32589c04e536a13908&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2019 C++Publisher:bio.tools Funded by:NIH | Microconnectomics of neoc..., WT | Sharing standardised expe..., NIH | Dissemination of a tool f... +6 projectsNIH| Microconnectomics of neocortex: a multiscale computer model ,WT| Sharing standardised experimental data and models of neural systems through the Open Source Brain repository ,NIH| Dissemination of a tool for data-driven multiscale modeling of brain circuits ,NIH| Dissemination of a tool for data-driven multiscale modeling of brain circuits ,NIH| Cortical and thalamic mechanisms of selective auditory attention ,EC| HBP SGA2 ,NIH| Embedded Ensemble Encoding ,WT| The Open Source Brain repository: enabling the collaborative development of open and accessible models for neuroscience ,NIH| Towards a Complete Description of the Circuitry Underlying Sharp Wave-Mediated Memory ReplayAuthors: Arkhipov, Anton;Arkhipov, Anton;Scalable Open Network Architecture TemplAte (SONATA) Data Format for Efficient Description of Large-Scale Network Models.
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For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=__bioTools__::a7c46e02d3db6f8c8648884fc5d9e6b4&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2019Publisher:bio.tools Funded by:EC | HBP SGA2, EC | HBP SGA1EC| HBP SGA2 ,EC| HBP SGA1Authors: Bjaalie, Jan G.; Laboratory, Neural Systems;Bjaalie, Jan G.; Laboratory, Neural Systems;Tool for user guided affine registration (anchoring) of 2D experimental image data, typically high resolution microscopic images, to 3D atlas reference space, facilitating data integration through standardized coordinate systems.
All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=__bioTools__::4bd00afcbf99211e0368956bd3d48cca&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=__bioTools__::4bd00afcbf99211e0368956bd3d48cca&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2019 RPublisher:bio.tools Funded by:EC | SYSCIDEC| SYSCIDAuthors: Yang, Wentao; Schulenburg, Hinrich;Yang, Wentao; Schulenburg, Hinrich;Using polynomial uncertainty modelling for differential gene expression estimation from RNA sequencing data.
All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=__bioTools__::0790acd95b029fec3879ef27df40b906&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=__bioTools__::0790acd95b029fec3879ef27df40b906&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2018 PythonPublisher:bio.tools Funded by:EC | RobustSynapses, EC | cis-CONTROLEC| RobustSynapses ,EC| cis-CONTROLAuthors: Davie, Kristofer; Waegeneer, Maxime De; Kreft, Lukasz;Davie, Kristofer; Waegeneer, Maxime De; Kreft, Lukasz;SCope is a fast visualization tool for large-scale and high dimensional scRNA-seq datasets. Currently the data format supported by SCope is .loom. This file format for very large omics datasets is maintained by the Linnarsson Lab through the loompy Python package (https://github.com/linnarsson-lab/loompy).
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For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=__bioTools__::ab10c610cf1ae816f52b6790b1e65d68&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2015 JavaPublisher:bio.tools Funded by:UKRI | Ensembl and enabling gene..., EC | HELIX NEBULA, WT +10 projectsUKRI| Ensembl and enabling genetics and genomics research in farmed animal species ,EC| HELIX NEBULA ,WT ,WT| Ensembl: current, complete and consistent annotation of large scale genome sequence ,NIH| GENCODE: comprehensive gene annotation for human and mouse ,EC| EURATRANS ,WT| Ensembl ,EC| QUANTOMICS ,NIH| Functional analysis of the zebrafish genome through RNA-seq and ribosome profile ,EC| BLUEPRINT ,UKRI| Ensembl and enabling genetics and genomics research in farmed animal species ,UKRI| Improving the rat reference genome annotation and building community engagement ,EC| SLINGAuthors: Flicek, Paul;Flicek, Paul;Genome databases for vertebrates genomes.
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For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=__bioTools__::cce9821dde6e5879dde269c0202e769b&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2015Publisher:bio.tools Funded by:EC | SISYPHE, EC | ALMONDEC| SISYPHE ,EC| ALMONDAuthors: Chikhi, Rayan; Rizk, Guillaume;Chikhi, Rayan; Rizk, Guillaume;Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.
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For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=__bioTools__::9c6366d5da24b30d7dca6e0b3b5f1ceb&type=result"></script>'); --> </script>
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