RNAseq_3rd_Party_Software.md
March 28, 2023 · View on GitHub
| 3rd Party Software Name | License | License URL | Copyright Notice |
|---|---|---|---|
| FastQC | GNU GENERAL PUBLIC LICENSE Version 2, June 1991 | https://github.com/s-andrews/FastQC/blob/master/LICENSE | Copyright (C) 1989, 1991 Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. |
| MultiQC | GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 | https://github.com/ewels/MultiQC/blob/master/LICENSE | Copyright (C) 2007 Free Software Foundation, Inc http://fsf.org/ Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. |
| Cutadapt | MIT License Copyright (c) 2010-2022 Marcel Martin | https://github.com/marcelm/cutadapt/blob/main/LICENSE | Copyright (c) 2010-2022 Marcel Martin marcel.martin@scilifelab.se Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: |
| samtools | The MIT/Expat License Copyright (C) 2008-2022 Genome Research Ltd. | https://github.com/samtools/samtools/blob/develop/LICENSE | Copyright (C) 2008-2022 Genome Research Ltd. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: |
| DESeq2 | GNU LESSER GENERAL PUBLIC LICENSE Version 3, 29 June 2007 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html | Copyright (C) 2007 Free Software Foundation, Inc. http://fsf.org/ Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. |
| RSeQC | GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 | http://rseqc.sourceforge.net | Copyright (C) 2007 Free Software Foundation, Inc. http://fsf.org/ Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. |
| TrimGalore | GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 | https://github.com/FelixKrueger/TrimGalore/blob/master/LICENSE | Copyright (C) 2007 Free Software Foundation, Inc. http://fsf.org/ Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. |
| R | GNU GENERAL PUBLIC LICENSE Version 2, June 1991, and Version 3, 29 June 2007 | https://www.r-project.org/Licenses/ | Version 2: Copyright (C) 1989, 1991 Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.; Version 3: Copyright (C) 2007 Free Software Foundation, Inc. http://fsf.org/ Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. |
| RSEM | GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 | https://github.com/deweylab/RSEM/blob/master/README.md#license | Copyright (C) 2007 Free Software Foundation, Inc. http://fsf.org/ Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. |
| gtfToGenePred | The MIT License (MIT) Copyright (C) 2001 UC Regents | https://github.com/ucscGenomeBrowser/kent/blob/master/LICENSE | Copyright (C) 2001 UC Regents. Permission is hereby granted, free of charge, to any person or non-commercial entity obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: |
| genePredToBed | The MIT License (MIT) Copyright (C) 2001 UC Regents | https://github.com/ucscGenomeBrowser/kent/blob/master/LICENSE | Copyright (C) 2001 UC Regents. Permission is hereby granted, free of charge, to any person or non-commercial entity obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: |
| tximport | GNU LESSER GENERAL PUBLIC LICENSE Version 2.1, February 1999 | https://github.com/mikelove/tximport/blob/master/DESCRIPTION | Copyright (C) 1991, 1999 Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. |
| tidyverse | The MIT License (MIT) Copyright (c) 2021 tidyverse authors | https://github.com/tidyverse/tidyverse/blob/main/LICENSE.md | Copyright (c) 2021 tidyverse authors. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: |
| stringr | MIT License Copyright (c) 2020 stringr authors | https://github.com/tidyverse/stringr/blob/main/LICENSE.md | Copyright (c) 2020 stringr authors Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: |
| STAR | The MIT License (MIT) Copyright (c) 2019 Alexander Dobin | https://github.com/alexdobin/STAR/blob/master/LICENSE | Copyright (c) 2019 Alexander Dobin. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: |
| dp_tools | The MIT License (MIT) Copyright (c) 2022 Jonathan Oribello | https://github.com/J-81/dp_tools/blob/main/LICENSE | Copyright (c) 2022 Jonathan Oribello. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: |
| Nextflow | Apache License Version 2.0, January 2004 | https://github.com/nextflow-io/nextflow/blob/master/COPYING | Grant of Copyright License. Subject to the terms and conditions of this License, each Contributor hereby grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable copyright license to reproduce, prepare Derivative Works of, publicly display, publicly perform, sublicense, and distribute the Work and such Derivative Works in Source or Object form. |
| Singularity | The BSD 3-clause License (MIT) Copyright (c) 2015-2017, Gregory M. Kurtzer. Copyright (c) 2016-2017, The Regents of the University of California. Copyright (c) 2017, SingularityWare, LLC. Copyright (c) 2018-2022, Sylabs, Inc. | https://docs.sylabs.io/guides/3.9/user-guide/license.html | Copyright (c) 2015-2017, Gregory M. Kurtzer. Copyright (c) 2016-2017, The Regents of the University of California. Copyright (c) 2017, SingularityWare, LLC. Copyright (c) 2018-2022, Sylabs, Inc. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: |
| python | The PSF LICENSE AGREEMENT Copyright (c) 2001-2022 Python Software Foundation | https://docs.python.org/3/license.html#psf-license-agreement-for-python-release | Copyright (c) 2001-2022 Python Software Foundation; All Rights Reserved |
| scipy | The BSD 3-Clause "New" or "Revised" License Copyright (c) 2001-2002 Enthought, Inc. 2003-2022, SciPy Developers. | https://github.com/scipy/scipy/blob/main/LICENSE.txt | Copyright (c) 2001-2002 Enthought, Inc. 2003-2022, SciPy Developers. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: |
| matplotlib | License agreement for matplotlib versions 1.3.0 and later Copyright (c) 2012-2022 Matplotlib Development Team; All Rights Reserved | https://matplotlib.org/stable/users/project/license.html | Copyright (c) 2012-2022 Matplotlib Development Team; All Rights Reserved |
| pandas | The BSD 3-clause License | https://github.com/pandas-dev/pandas/blob/main/LICENSE | Copyright (c) 2008-2011, AQR Capital Management, LLC, Lambda Foundry, Inc. and PyData Development Team; All rights reserved. Copyright (c) 2011-2022, Open source contributors. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: |
| numpy | The BSD 3-clause License Copyright (c) 2005-2022, NumPy Developers. | https://github.com/numpy/numpy/blob/main/LICENSE.txt | Copyright (c) 2005-2022, NumPy Developers. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: |
| seaborn | The BSD 3-clause License Copyright (c) 2012-2021, Michael L. Waskom | https://github.com/mwaskom/seaborn/blob/master/LICENSE.md | Copyright (c) 2012-2021, Michael L. Waskom All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: |
| jupyter notebook | Modified BSD License Copyright (c) 2001-2015, IPython Development Team, Copyright (c) 2015-, Jupyter Development Team | https://github.com/jupyter/notebook/blob/main/LICENSE | - Copyright (c) 2001-2015, IPython Development Team - Copyright (c) 2015-, Jupyter Development Team All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: |
| loguru | MIT License Copyright (c) 2017 | https://github.com/Delgan/loguru/blob/master/LICENSE | MIT License Copyright (c) 2017 Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: |
| pandera | MIT License Copyright (c) 2018 Niels Bantilan | https://github.com/unionai-oss/pandera/blob/main/LICENSE.txt | MIT License Copyright (c) 2018 Niels Bantilan Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: |