Adding updated Amplicon Illumina Sequencing Pipeline, GL-DPPD-7104-B

Author: asaravia-butler

3rd_Party_Licenses/Amplicon_and_Metagenomics_3rd_Party_Software.md

@@ -26,3 +26,12 @@
 |Snakemake|[The MIT License (MIT) Copyright (c) 2012-2019 Johannes Köster](Amplicon_and_Metagenomics_3rd_Party_Software_Licenses/License_Snakemake_6.7.0_documentation.pdf)|[https://snakemake.readthedocs.io/en/stable/project_info/license.html](https://snakemake.readthedocs.io/en/stable/project_info/license.html)|Copyright (c) 2012-2019 Johannes Köster <johannes.koester@tu-dortmund.de> 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:|
 |genelab-utils|[GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007](Amplicon_and_Metagenomics_3rd_Party_Software_Licenses/genelab-utils_LICENSE.pdf)|[https://github.com/AstrobioMike/GeneLab-utils/blob/main/LICENSE](https://github.com/AstrobioMike/GeneLab-utils/blob/main/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.|
 |KEGGDecoder|[The MIT License (MIT) Copyright (c) 2019 Benjamin Tully](Amplicon_and_Metagenomics_3rd_Party_Software_Licenses/KEGGDecoder_LICENSE.pdf)|[https://github.com/bjtully/BioData/blob/master/LICENSE](https://github.com/bjtully/BioData/blob/master/LICENSE) | Copyright (c) 2019 Benjamin Tully 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:|
+|R|[GNU GENERAL PUBLIC LICENSE Version 2, June 1991, and Version 3, 29 June 2007](Amplicon_and_Metagenomics_3rd_Party_Software_Licenses/R_GPL-2_and_GPL-3_LICENSES.pdf)|[https://www.r-project.org/Licenses/](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.|
+|vegan|[GNU GENERAL PUBLIC LICENSE Version 2, June 1991](Amplicon_and_Metagenomics_3rd_Party_Software_Licenses/vegan_LICENSE.pdf)|[https://github.com/vegandevs/vegan/blob/master/LICENSE](https://github.com/vegandevs/vegan/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.|
+|tidyverse|[MIT Licence Copyright (c) 2021](Amplicon_and_Metagenomics_3rd_Party_Software_Licenses/tidyverse_LICENSE.pdf)|[https://tidyverse.tidyverse.org/LICENSE.html](https://tidyverse.tidyverse.org/LICENSE.html)|MIT License Copyright (c) 2021 tidyverse authors|
+|dendextend|[GNU GENERAL PUBLIC LICENSE Version 2, June 1991, and Version 3, 29 June 2007](Amplicon_and_Metagenomics_3rd_Party_Software_Licenses/R_GPL-2_and_GPL-3_LICENSES.pdf)|[https://talgalili.github.io/dendextend/](https://talgalili.github.io/dendextend/)|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.| 
+|ggrepel|[GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007](Amplicon_and_Metagenomics_3rd_Party_Software_Licenses/ggrepel_LICENSE.pdf)|[https://github.com/slowkow/ggrepel/blob/master/LICENSE](https://github.com/slowkow/ggrepel/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.|
+|dplyr|[MIT License Copyright (c) 2022 dplyr authors](Amplicon_and_Metagenomics_3rd_Party_Software_Licenses/dplyr_LICENSE.pdf)|[https://github.com/tidyverse/dplyr/blob/main/LICENSE.md](https://github.com/tidyverse/dplyr/blob/main/LICENSE.md)|Copyright (c) 2022 dplyr 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:|
+|rcolorbrewer|[Apache License Version 2.0, January 2004](Amplicon_and_Metagenomics_3rd_Party_Software_Licenses/colorbrewer_LICENSE.pdf)|[https://github.com/axismaps/colorbrewer/blob/master/LICENCE.txt](https://github.com/axismaps/colorbrewer/blob/master/LICENCE.txt)|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.|
+|DESeq2|[GNU LESSER GENERAL PUBLIC LICENSE Version 3, 29 June 2007](Amplicon_and_Metagenomics_3rd_Party_Software_Licenses/DESeq2_LICENSE.pdf)|[https://bioconductor.org/packages/release/bioc/html/DESeq2.html](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.|
+|phyloseq|[GNU AFFERO GENERAL PUBLIC LICENSE Version 3, 19 November 2007](Amplicon_and_Metagenomics_3rd_Party_Software_Licenses/phyloseq_LICENSE.pdf)|[https://bioconductor.org/packages/release/bioc/html/phyloseq.html](https://bioconductor.org/packages/release/bioc/html/phyloseq.html)|Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/> Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.|