781 Research products

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muCNV
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2021 C++ bio.tools NIH | Genomic Architecture of C..., NIH | The Baylor-Hopkins Clinic...
Authors: Jun, Goo;
Jun, Goo;
muCNV is genotyping structural variants for population-level sequencingMulti-sample SV genotyper for large-scale WGS data. muCNV uses multiple steps for multi-sample SV genotyping, to handle large number of samples and to enable efficient parallelization:.
bio.toolsarrow_drop_down
bio.tools
Software . 2021
License: MIT
Data sources: bio.tools
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bio.tools
Software . 2021
License: MIT
Data sources: bio.tools
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MDTS
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2018 R bio.tools NIH | Molecular Genetic Epidemi..., NIH | Sequencing of significant..., WT
Authors: Fu, Jack M.;
Fu, Jack M.;
A package for the detection of de novo copy number deletions in targeted sequencing of trios with high sensitivity and positive predictive value.
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bio.tools
Software . 2018
License: Artistic-2.0
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2018
License: Artistic-2.0
Data sources: bio.tools
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bioassayR
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2017 R bio.tools NIH | Integrative Resource to D..., NSF | ChemMine Tools: an Open S...
Authors: Backman, Tyler;
Backman, Tyler;
Computational tool that enables simultaneous analysis of thousands of bioassay experiments performed over a diverse set of compounds and biological targets. Unique features include support for large-scale cross-target analyses of both public and custom bioassays, generation of high throughput screening fingerprints (HTSFPs), and an optional preloaded database that provides access to a substantial portion of publicly available bioactivity data.
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bio.tools
Software . 2017
License: Artistic-2.0
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bio.tools
Software . 2017
License: Artistic-2.0
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COSS
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019 Java bio.tools NIH | A Galaxy?based multi?omic..., EC | EPIC-XS
Authors: Group, Computational Omics and Systems Biology;
Group, Computational Omics and Systems Biology;
COSS (CompOmics Spectral Searching ) is a user-friendly spectral library search tool capable of processing large spectral libraries and supporting multiple file formats.
bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: Apache-2.0
Data sources: bio.tools
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bio.tools
Software . 2019
License: Apache-2.0
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IGS (CMTK) Image Registration Tools Classic MacOSX GUI (2008-10-10)
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2012Zenodo EC | OlfSwitch, NIH | Neuroimaging of Alcohol-i..., NIH | Assembly of the Central O...
Authors: Jefferis, Gregory;
Jefferis, Gregory;
doi: 10.5281/zenodo.1193266 , 10.5281/zenodo.1193268 , 10.5281/zenodo.1193267 , 10.5281/zenodo.1193265
doi: 10.5281/zenodo.1193266 , 10.5281/zenodo.1193268 , 10.5281/zenodo.1193267 , 10.5281/zenodo.1193265
This is the classic MacOSX GUI for the CMTK registration tools (formerly called IGS suite). This is a frontend for software developed at https://www.nitrc.org/projects/cmtk. Please see http://flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=warping_manual:registration_gui for instructions on how to carry out image registration.
ZENODOarrow_drop_down
ZENODO
Software . 2011
License: http://creativecommons.org/licenses/by/4.0/legalcode
Data sources: ZENODO
ZENODO
Software . 2012
License: http://creativecommons.org/licenses/by/4.0/legalcode
Data sources: ZENODO
ZENODO
Software . 2012
License: https://creativecommons.org/licenses/by/4.0/legalcode
Data sources: Datacite
ZENODO
Software . 2008
License: http://creativecommons.org/licenses/by/4.0/legalcode
Data sources: ZENODO
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ZENODOarrow_drop_down
ZENODO
Software . 2011
License: http://creativecommons.org/licenses/by/4.0/legalcode
Data sources: ZENODO
ZENODO
Software . 2012
License: http://creativecommons.org/licenses/by/4.0/legalcode
Data sources: ZENODO
ZENODO
Software . 2012
License: https://creativecommons.org/licenses/by/4.0/legalcode
Data sources: Datacite
ZENODO
Software . 2008
License: http://creativecommons.org/licenses/by/4.0/legalcode
Data sources: ZENODO
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GWASTools
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2017 R bio.tools NIH | Genome Wide Association C..., NIH | Randomized Clinical Trial...
Authors: Gogarten, Stephanie M.; Stilp, Adrienne;
Gogarten, Stephanie M.; Stilp, Adrienne;
Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.
bio.toolsarrow_drop_down
bio.tools
Software . 2017
License: Artistic-2.0
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2017
License: Artistic-2.0
Data sources: bio.tools
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16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2017 English Code Ocean NIH | A Software Framework for ..., NIH | Computational Methods for...
Authors: Ruibang Luo;
Ruibang Luo;
doi: 10.24433/co.0a812d9b-0ff3-4eb7-825f-76d3cd049a43
doi: 10.24433/co.0a812d9b-0ff3-4eb7-825f-76d3cd049a43
16GT is a variant caller utilizing a 16-genotype probabilistic model to unify SNP and indel calling in a single algorithm. 16GT is easy to use. The default parameters will fit most of the use cases with human genome. For the detailed parameters for each module, please run the module to get an info.
Code Oceanarrow_drop_down
Code Ocean
Software . 2017
License: https://opensource.org/licenses/MIT
Data sources: Datacite
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Code Oceanarrow_drop_down
Code Ocean
Software . 2017
License: https://opensource.org/licenses/MIT
Data sources: Datacite
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Lilikoi
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019 R bio.tools NIH | An Integrative Omics Appr..., NIH | An Integrative Bioinforma..., NIH | An Integrative Bioinforma...
Authors: Alakwaa, Fadhl;
Alakwaa, Fadhl;
R package for personalized pathway-based classification modeling using metabolomics data.
bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: GPL-2.0
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: GPL-2.0
Data sources: bio.tools
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CoBE_VSE (Variant Set Enrichment example)
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2021 English Code Ocean NIH | Bioinformatics Strategies..., NIH | Breast and prostate cance..., NIH | Machine Learning Predicti...
Authors: Ankita Nand;
Ankita Nand;
doi: 10.24433/co.2261649.v2 , 10.24433/co.2261649.v1
doi: 10.24433/co.2261649.v2 , 10.24433/co.2261649.v1
This is an example capsule for CoBE(https://www.pmcobe.ca) executable. The capsule is made using software, source code and data coming from public sources and other authors. Please find the original links for code/data in capsule description below: https://biodatamining.biomedcentral.com/articles/10.1186/s13040-017-0129-5 https://github.com/LupienLab/VSE
Code Oceanarrow_drop_down
Code Ocean
Software . 2021
License: http://www.apache.org/licenses/LICENSE-2.0
Data sources: Datacite
Code Ocean
Software . 2022
License: http://www.apache.org/licenses/LICENSE-2.0
Data sources: Datacite
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Code Oceanarrow_drop_down
Code Ocean
Software . 2021
License: http://www.apache.org/licenses/LICENSE-2.0
Data sources: Datacite
Code Ocean
Software . 2022
License: http://www.apache.org/licenses/LICENSE-2.0
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bnbc
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2018Bioconductor NIH | Cancer Genomics: Integrat..., NIH | Additional Data Generatio...
Authors: Fletez-Brant, Kipper;
Fletez-Brant, Kipper;
doi: 10.18129/b9.bioc.bnbc
doi: 10.18129/b9.bioc.bnbc
Tools to normalize (several) Hi-C data from replicates.
bio.toolsarrow_drop_down
bio.tools
Software . 2018
License: Artistic-2.0
Data sources: bio.tools
https://doi.org/10.18129/b9.bi...
Software . 2017
Data sources: Datacite
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bio.toolsarrow_drop_down
bio.tools
Software . 2018
License: Artistic-2.0
Data sources: bio.tools
https://doi.org/10.18129/b9.bi...
Software . 2017
Data sources: Datacite
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781 Research products

muCNV
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2021 C++ bio.tools NIH | Genomic Architecture of C..., NIH | The Baylor-Hopkins Clinic...
Authors: Jun, Goo;
Jun, Goo;
muCNV is genotyping structural variants for population-level sequencingMulti-sample SV genotyper for large-scale WGS data. muCNV uses multiple steps for multi-sample SV genotyping, to handle large number of samples and to enable efficient parallelization:.
bio.toolsarrow_drop_down
bio.tools
Software . 2021
License: MIT
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2021
License: MIT
Data sources: bio.tools
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MDTS
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2018 R bio.tools NIH | Molecular Genetic Epidemi..., NIH | Sequencing of significant..., WT
Authors: Fu, Jack M.;
Fu, Jack M.;
A package for the detection of de novo copy number deletions in targeted sequencing of trios with high sensitivity and positive predictive value.
bio.toolsarrow_drop_down
bio.tools
Software . 2018
License: Artistic-2.0
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2018
License: Artistic-2.0
Data sources: bio.tools
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bioassayR
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2017 R bio.tools NIH | Integrative Resource to D..., NSF | ChemMine Tools: an Open S...
Authors: Backman, Tyler;
Backman, Tyler;
Computational tool that enables simultaneous analysis of thousands of bioassay experiments performed over a diverse set of compounds and biological targets. Unique features include support for large-scale cross-target analyses of both public and custom bioassays, generation of high throughput screening fingerprints (HTSFPs), and an optional preloaded database that provides access to a substantial portion of publicly available bioactivity data.
bio.toolsarrow_drop_down
bio.tools
Software . 2017
License: Artistic-2.0
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2017
License: Artistic-2.0
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COSS
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019 Java bio.tools NIH | A Galaxy?based multi?omic..., EC | EPIC-XS
Authors: Group, Computational Omics and Systems Biology;
Group, Computational Omics and Systems Biology;
COSS (CompOmics Spectral Searching ) is a user-friendly spectral library search tool capable of processing large spectral libraries and supporting multiple file formats.
bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: Apache-2.0
Data sources: bio.tools
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bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: Apache-2.0
Data sources: bio.tools
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IGS (CMTK) Image Registration Tools Classic MacOSX GUI (2008-10-10)
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2012Zenodo EC | OlfSwitch, NIH | Neuroimaging of Alcohol-i..., NIH | Assembly of the Central O...
Authors: Jefferis, Gregory;
Jefferis, Gregory;
doi: 10.5281/zenodo.1193266 , 10.5281/zenodo.1193268 , 10.5281/zenodo.1193267 , 10.5281/zenodo.1193265
doi: 10.5281/zenodo.1193266 , 10.5281/zenodo.1193268 , 10.5281/zenodo.1193267 , 10.5281/zenodo.1193265
This is the classic MacOSX GUI for the CMTK registration tools (formerly called IGS suite). This is a frontend for software developed at https://www.nitrc.org/projects/cmtk. Please see http://flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=warping_manual:registration_gui for instructions on how to carry out image registration.
ZENODOarrow_drop_down
ZENODO
Software . 2011
License: http://creativecommons.org/licenses/by/4.0/legalcode
Data sources: ZENODO
ZENODO
Software . 2012
License: http://creativecommons.org/licenses/by/4.0/legalcode
Data sources: ZENODO
ZENODO
Software . 2012
License: https://creativecommons.org/licenses/by/4.0/legalcode
Data sources: Datacite
ZENODO
Software . 2008
License: http://creativecommons.org/licenses/by/4.0/legalcode
Data sources: ZENODO
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1
citations 1
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visibility333
visibility views 333
download downloads 89
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ZENODOarrow_drop_down
ZENODO
Software . 2011
License: http://creativecommons.org/licenses/by/4.0/legalcode
Data sources: ZENODO
ZENODO
Software . 2012
License: http://creativecommons.org/licenses/by/4.0/legalcode
Data sources: ZENODO
ZENODO
Software . 2012
License: https://creativecommons.org/licenses/by/4.0/legalcode
Data sources: Datacite
ZENODO
Software . 2008
License: http://creativecommons.org/licenses/by/4.0/legalcode
Data sources: ZENODO
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GWASTools
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2017 R bio.tools NIH | Genome Wide Association C..., NIH | Randomized Clinical Trial...
Authors: Gogarten, Stephanie M.; Stilp, Adrienne;
Gogarten, Stephanie M.; Stilp, Adrienne;
Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.
bio.toolsarrow_drop_down
bio.tools
Software . 2017
License: Artistic-2.0
Data sources: bio.tools
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bio.tools
Software . 2017
License: Artistic-2.0
Data sources: bio.tools
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16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2017 English Code Ocean NIH | A Software Framework for ..., NIH | Computational Methods for...
Authors: Ruibang Luo;
Ruibang Luo;
doi: 10.24433/co.0a812d9b-0ff3-4eb7-825f-76d3cd049a43
doi: 10.24433/co.0a812d9b-0ff3-4eb7-825f-76d3cd049a43
16GT is a variant caller utilizing a 16-genotype probabilistic model to unify SNP and indel calling in a single algorithm. 16GT is easy to use. The default parameters will fit most of the use cases with human genome. For the detailed parameters for each module, please run the module to get an info.
Code Oceanarrow_drop_down
Code Ocean
Software . 2017
License: https://opensource.org/licenses/MIT
Data sources: Datacite
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Code Ocean
Software . 2017
License: https://opensource.org/licenses/MIT
Data sources: Datacite
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Lilikoi
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2019 R bio.tools NIH | An Integrative Omics Appr..., NIH | An Integrative Bioinforma..., NIH | An Integrative Bioinforma...
Authors: Alakwaa, Fadhl;
Alakwaa, Fadhl;
R package for personalized pathway-based classification modeling using metabolomics data.
bio.toolsarrow_drop_down
bio.tools
Software . 2019
License: GPL-2.0
Data sources: bio.tools
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bio.tools
Software . 2019
License: GPL-2.0
Data sources: bio.tools
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CoBE_VSE (Variant Set Enrichment example)
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2021 English Code Ocean NIH | Bioinformatics Strategies..., NIH | Breast and prostate cance..., NIH | Machine Learning Predicti...
Authors: Ankita Nand;
Ankita Nand;
doi: 10.24433/co.2261649.v2 , 10.24433/co.2261649.v1
doi: 10.24433/co.2261649.v2 , 10.24433/co.2261649.v1
This is an example capsule for CoBE(https://www.pmcobe.ca) executable. The capsule is made using software, source code and data coming from public sources and other authors. Please find the original links for code/data in capsule description below: https://biodatamining.biomedcentral.com/articles/10.1186/s13040-017-0129-5 https://github.com/LupienLab/VSE
Code Oceanarrow_drop_down
Code Ocean
Software . 2021
License: http://www.apache.org/licenses/LICENSE-2.0
Data sources: Datacite
Code Ocean
Software . 2022
License: http://www.apache.org/licenses/LICENSE-2.0
Data sources: Datacite
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Code Ocean
Software . 2021
License: http://www.apache.org/licenses/LICENSE-2.0
Data sources: Datacite
Code Ocean
Software . 2022
License: http://www.apache.org/licenses/LICENSE-2.0
Data sources: Datacite
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bnbc
integration_instructionsResearch softwarekeyboard_double_arrow_right Software 2018Bioconductor NIH | Cancer Genomics: Integrat..., NIH | Additional Data Generatio...
Authors: Fletez-Brant, Kipper;
Fletez-Brant, Kipper;
doi: 10.18129/b9.bioc.bnbc
doi: 10.18129/b9.bioc.bnbc
Tools to normalize (several) Hi-C data from replicates.
bio.toolsarrow_drop_down
bio.tools
Software . 2018
License: Artistic-2.0
Data sources: bio.tools
https://doi.org/10.18129/b9.bi...
Software . 2017
Data sources: Datacite
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Software . 2018
License: Artistic-2.0
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Software . 2017
Data sources: Datacite
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