Source: https://docs.nygen.io/CyteArc/reference/third-party-notices/ Revision: 2edce5ebd82eeb3a47bfe8d929e59bf5aa01d843 Structured page: https://docs.nygen.io/CyteArc/reference.third-party-notices.json Third-party notices CyteArc is copyright Nygen Analytics AB and is licensed under the BSD 3-Clause License in the LICENSE file. Parts of CyteArc derive from the third-party software listed below, and the repository includes a font and small excerpts of public data. Each keeps its own license, and the full license texts are at the end of this file. The dataset sections credit the data that the documentation and tests download, and a later section lists optional packages that CyteArc can use but does not install. Software Scanpy Source: https://github.com/scverse/scanpy Copyright (c) 2025 scverse®; Copyright (c) 2017 F. Alexander Wolf, P. Angerer, Theis Lab License: BSD-3-Clause Used in: cytearc/features/scoring.py (gene-set scoring adapted from score_genes), cytearc/datastore/_operations/quality_control.py (the control-set size of cell-cycle scoring), and the categorical palettes in cytearc/plotting/_style.py. umap-learn Source: https://github.com/lmcinnes/umap Copyright (c) 2017, Leland McInnes License: BSD-3-Clause Used in: cytearc/embeddings/umap.py (the densMAP density terms and the fuzzy set union) and the UMAP parameter descriptions in cytearc/datastore/_operations/embeddings.py. Seurat Source: https://github.com/satijalab/seurat Copyright (c) 2021 Seurat authors License: MIT Used in: cytearc/neighbors/integration.py (the modality weights and constants of FindModalityWeights and MultiModalNN), cytearc/quality_control/hto.py (the HTODemux procedure), scripts/export_seurat_wnn_golden.R (expressions copied from FindModalityWeights), and the reference equations in tests/test_knn_utils.py. chromVAR Source: https://github.com/GreenleafLab/chromVAR Copyright (c) 2017 Stanford University License: MIT Used in: cytearc/features/enrichment/chromvar.py (background-peak sampling translated from getBackgroundPeaks, and the deviation computation) and tests/test_enrichment_chromvar.py (chromVAR’s test inputs and expected values). MOODS Source: https://github.com/jhkorhonen/MOODS Copyright (C) 2007-2015 Pasi Rastas, Janne H. Korhonen, Petri Martinmäki License: MOODS is licensed under the GPL-3.0-or-later or the Biopython License Agreement, at the recipient’s choice. CyteArc uses it under the Biopython License Agreement. Used in: cytearc/features/genomic/motifs.py (log-odds scoring, min_delta, and the p-value threshold computation, translated from core/moods_tools.cpp). BPCells Source: https://github.com/bnprks/BPCells Copyright (c) 2021-2023 BPCells contributors License: BPCells is licensed under the Apache-2.0 or the MIT License, at the recipient’s choice. CyteArc uses it under the MIT License. Used in: cytearc/readers/_seurat/operations.py (_rank_values follows ColwiseRank). decoupler Source: https://github.com/scverse/decoupler Copyright (c) 2025, scverse®; Copyright (c) 2025, Pau Badia i Mompel, Saez lab License: BSD-3-Clause Used in: cytearc/features/enrichment/aucell.py (the AUC kernel and the n_up default). arboreto Source: https://github.com/aertslab/arboreto Copyright (c) 2017, Thomas Moerman License: BSD-3-Clause Used in: cytearc/regulons/grn.py (the early-stopping monitor, the GRNBoost2 defaults, and the importance scaling). SciPy Source: https://github.com/scipy/scipy Copyright (c) 2001-2002 Enthought, Inc. 2003, SciPy Developers. License: BSD-3-Clause Used in: cytearc/features/markers/regression.py (the correlation and its p-value, adapted from scipy.stats.linregress). scib-metrics Source: https://github.com/YosefLab/scib-metrics Copyright (c) 2022, Adam Gayoso License: BSD-3-Clause Used in: cytearc/metrics/lisi.py (the names, defaults, and scaling of ilisi_knn and clisi_knn). EoN (Epidemics on Networks) Source: https://github.com/springer-math/Mathematics-of-Epidemics-on-Networks Copyright (c) 2016 Joel C Miller License: MIT Used in: cytearc/plotting/cluster_tree.py (_hierarchy_positions, the tree layout adapted from hierarchy_pos). scikit-learn Source: https://github.com/scikit-learn/scikit-learn Copyright (c) 2007-2026 The scikit-learn developers. License: BSD-3-Clause Used in: tests/paris_quality_gate.py (the adjusted Rand index in scikit-learn’s pair-confusion form). This is test code and is not part of the installed package. Fonts Inter Source: https://github.com/rsms/inter (version 4.1, unmodified) Copyright (c) 2016 The Inter Project Authors (https://github.com/rsms/inter ) License: SIL Open Font License 1.1 Used in: cytearc/agent/report_assets.py. Every HTML report that CyteArc generates embeds the font and keeps its license in a source comment. Data in this repository JASPAR (https://jaspar.elixir.no ), CC BY 4.0: the motif matrices MA0004.1 (Arnt) and MA0006.1 (Ahr::Arnt), and an excerpt of the MEME export of MA0004.1, in tests/test_genomic_motifs.py. Rauluseviciute et al. (2024), Nucleic Acids Research, doi:10.1093/nar/gkad1059. 10x Genomics, CC BY 4.0: tests/seurat_wnn_5_5_1_golden.json holds Seurat 5.5.1 outputs on principal components of 300 cells of the tenx_8K_pbmc_citeseq dataset, and the reference images in tests/visual/showcase/ are rendered from the 1k PBMC CITE-seq test fixture. Both datasets are credited below. GEO GSE245108: hashtag counts in tests/seurat_hto_5_5_1_golden.json, from Zhang et al. (2024), Nature Immunology, doi:10.1038/s41590-024-01782-4. Color palettes in cytearc/plotting/_style.py: the 10- and 20-color sets are Tableau 10 and 20 as distributed with matplotlib (the 10-color set with Scanpy’s colorblind substitutions), the 28-color set is from Zeileis, Hornik, and Murrell (2009), Computational Statistics & Data Analysis, doi:10.1016/j.csda.2008.11.033, and the 102-color set is from Tatarize’s “Color Distribution Methodology”. All four are as compiled in Scanpy. Example datasets cytearc.datasets.connect("cytearc_docs") downloads these from Nygen’s public Nygen/cytebase bucket on Hugging Face. They are not part of the CyteArc package. Nygen converted each source to a CyteArc store and analyzed it, and the manifest.json file next to each store records the steps. Cite the original studies when you use the data. Dataset Source License or terms tenx_5K_pbmc_rnaseq “5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor (v3 chemistry)”, 10x Genomics, https://www.10xgenomics.com/datasets CC BY 4.0 tenx_8K_pbmc_citeseq “10k PBMCs from a Healthy Donor - Gene Expression and Cell Surface Protein”, 10x Genomics, https://www.10xgenomics.com/datasets CC BY 4.0 tenx_10K_pbmc-v1_atacseq “10k Peripheral blood mononuclear cells (PBMCs) from a healthy donor”, Single Cell ATAC v1.0, 10x Genomics, https://www.10xgenomics.com/datasets CC BY 4.0 tenx_1.3M_brain_rnaseq “1.3 Million Brain Cells from E18 Mice”, 10x Genomics, https://www.10xgenomics.com/datasets . Unmodified Cell Ranger matrix CC BY 4.0 kang_15K_pbmc_rnaseq, kang_14K_ifnb-pbmc_rnaseq, kang_29K_ctrl-ifnb_pbmc_rnaseq Kang et al. (2018), Nature Biotechnology 36:89-94, doi:10.1038/nbt.4042; GEO GSE96583 GEO; no license stated bastidas-ponce_4K_pancreas-d15_rnaseq Bastidas-Ponce et al. (2019), Development 146:dev173849, doi:10.1242/dev.173849; GEO GSE132188. The processed file data/Pancreas/endocrinogenesis_day15.h5ad comes from the Theis lab repository https://github.com/theislab/scvelo_notebooks , published with scVelo (Bergen et al. (2020), Nature Biotechnology, doi:10.1038/s41587-020-0591-3) GEO; the processed file states no license xin_1K_pancreas_rnaseq Xin et al. (2016), Cell Metabolism 24:608-615, doi:10.1016/j.cmet.2016.08.018; GEO GSE81608 GEO; no license stated swanson_7K_pbmc_teaseq Swanson et al. (2021), eLife 10:e63632, doi:10.7554/eLife.63632. Built from GSM5123951_PBMC_permcells_TEA-seq_SeuratObject.rds by Lucas Graybuck, Elliott Swanson, and Peter Skene (Zenodo, doi:10.5281/zenodo.6360802) and the paper’s Figure 4 source data 2 CC BY 4.0 tabula_sapiens, tabula_sapiens_100k The Tabula Sapiens Consortium (2024), bioRxiv, doi:10.1101/2024.12.03.626516; “Tabula Sapiens - All Cells” from CZ CELLxGENE Discover, https://cellxgene.cziscience.com/collections/e5f58829-1a66-40b5-a624-9046778e74f5 . tabula_sapiens_100k is a 100,000-cell sample CC BY 4.0, and the Tabula Sapiens Data Release Policy, https://tabula-sapiens.sf.czbiohub.org/whereisthedata , whose full text is in each store’s manifest annotations Gene-body coordinates derived from GENCODE, Frankish et al. (2023), Nucleic Acids Research, doi:10.1093/nar/gkac1071 No restrictions stated CC BY 4.0 is the Creative Commons Attribution 4.0 International license, https://creativecommons.org/licenses/by/4.0/ . Test datasets tests/download_fixtures.py downloads these from the same bucket. They are not part of the CyteArc package. File Source License or terms 1K_pbmc_citeseq.h5 “1k Human PBMCs with TotalSeq-B Human TBNK Antibody Cocktail, 3’ LT v3.1”, 10x Genomics, https://www.10xgenomics.com/datasets . Unmodified filtered matrix CC BY 4.0 500_pbmc_atac.zarr.tar.gz “500 Peripheral Blood Mononuclear Cells (PBMCs) from a Healthy Donor (Next GEM v1.1)”, 10x Genomics, https://www.10xgenomics.com/datasets . Converted to a CyteArc store CC BY 4.0 cell_attributes.csv, knn_*.npy, atac_knn_*.npy, markers_cluster1.csv, pseudotime_*, aggregated_*, ptime_modules_group_1.npy Analysis outputs computed from the two 10x Genomics datasets above CC BY 4.0 toy_cr_dir.tar.gz, toy_cr_dir_empty.tar.gz Synthetic Cell Ranger-style directories BSD-3-Clause, as in LICENSE seurat_assay5_synthetic.rds tests/data/synthetic.rds from https://github.com/harryhaller001/readseurat at commit 8a688b47df27f90e98a4c57ddd9e47c0e5ded01e MIT, Copyright (c) 2026 harryhaller001 seurat_v4_1_3_pbmc_mye.rds pbmc10k_mye_small_velocyto.rds by Hua Yichao, SeuratExtend example data (Zenodo, doi:10.5281/zenodo.10944066), derived from 10x Genomics PBMC data CC0 1.0; the underlying 10x Genomics data are CC BY 4.0 Data that tutorials download from their publishers Tutorial Source License or terms Regulons and gene programs “PBMC from a Healthy Donor - Granulocytes Removed Through Cell Sorting (3k)”, Single Cell Multiome ATAC + Gene Expression, 10x Genomics, https://www.10xgenomics.com/datasets CC BY 4.0 Regulons and gene programs cisTarget ranking database, motif-to-factor table, and factor list from the Stein Aerts lab, https://resources.aertslab.org/cistarget/ No terms stated. The v10 motif collection includes motifs derived from TRANSFAC Professional, a commercial database, so confirm the terms before commercial use Regulons and gene programs JASPAR 2024 CORE vertebrate motifs, Rauluseviciute et al. (2024), Nucleic Acids Research, doi:10.1093/nar/gkad1059 CC BY 4.0 Regulons and gene programs GENCODE release 32 genome and annotation, Frankish et al. (2023), Nucleic Acids Research, doi:10.1093/nar/gkac1071 No restrictions stated Regulons and gene programs SPI1 CUT&RUN peaks of experiment SRX26995709 from ChIP-Atlas, Zou et al. (2024), Nucleic Acids Research, doi:10.1093/nar/gkae358. ChIP-Atlas (c) Shinya Oki (Kyoto University) licensed under CC Attribution-Share Alike 4.0 International CC BY-SA 4.0, https://creativecommons.org/licenses/by-sa/4.0/ Harmony batch correction, Donor-level comparisons, Pseudobulk export Binvignat et al. (2024), JCI Insight, doi:10.1172/jci.insight.178499, from CZ CELLxGENE Discover, https://cellxgene.cziscience.com/collections/e1a9ca56-f2ee-435d-980a-4f49ab7a952b CC BY 4.0 HTO demultiplexing Stoeckius et al. (2018), Genome Biology 19:224, doi:10.1186/s13059-018-1603-1; GEO GSE108313 (GSM2895282, GSM2895283) GEO; no license stated CyteBase datasets and CyteBase composite datasets Datasets from CZ CELLxGENE Discover, each credited in its CyteBase catalog entry The license of each dataset on CELLxGENE Discover, usually CC BY 4.0 Optional packages that CyteArc does not install CyteArc contains no code from these GPL-licensed packages, and its default installation does not include them: sgtsnepi (GPL-3.0) computes t-SNE. The tsne extra installs it, and the test and docs extras install it on Linux x86_64. igraph (GPL-2.0-or-later) and leidenalg (GPL-3.0-or-later) serve the optional "igraph" and "leidenalg" Leiden backends. No CyteArc extra installs them. License texts Scanpy BSD 3-Clause License Copyright (c) 2025 scverse® Copyright (c) 2017 F. Alexander Wolf, P. Angerer, Theis Lab All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. umap-learn BSD 3-Clause License Copyright (c) 2017, Leland McInnes All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Seurat # MIT License Copyright (c) 2021 Seurat 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: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. chromVAR Copyright (c) 2017 Stanford University 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: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. MOODS (Biopython License Agreement) Biopython License Agreement Permission to use, copy, modify, and distribute this software and its documentation with or without modifications and for any purpose and without fee is hereby granted, provided that any copyright notices appear in all copies and that both those copyright notices and this permission notice appear in supporting documentation, and that the names of the contributors or copyright holders not be used in advertising or publicity pertaining to distribution of the software without specific prior permission. THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. BPCells (MIT License) Copyright (c) 2021-2023 BPCells contributors 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: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. decoupler BSD 3-Clause License Copyright (c) 2025, scverse® Copyright (c) 2025, Pau Badia i Mompel, Saez lab All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. arboreto BSD 3-Clause License Copyright (c) 2017, Thomas Moerman All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. SciPy Copyright (c) 2001-2002 Enthought, Inc. 2003, 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: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. scib-metrics BSD 3-Clause License Copyright (c) 2022, Adam Gayoso All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 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EoN Copyright (c) 2016 Joel C Miller 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: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. 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Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.