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# %% [markdown] # # Welcome to the AIMS Jupyter Notebook! # # As a refresher, hit ctrl + enter to run each cell # I tried to add comments and other markdown cells like this one where appropriate to help with interpretations # %% [markdown] # # Section 0: Loading in Modules and Defining Figure Formatting # This first c...
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# %% [markdown] # # Training from CV folds # # Loads folds saved either as `cv_folds.pkl` or as per-fold pickles in a directory named `folds_interaction-type`. Trains an MLP per fold and reports fold-wise metrics and mean ± std. # %% import os os.environ["CUDA_DEVICE_ORDER"]="PCI_BUS_ID" os.environ["CUDA_VISIBLE_DEVI...
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# %% import pickle import numpy as np import matplotlib as mpl import matplotlib.pyplot as plt import os import tqdm import scipy from scipy import signal from tqdm import tnrange import seaborn as sns from scipy.stats import norm,entropy,linregress from scipy.optimize import minimize, curve_fit from scipy.io import sa...
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# %% [markdown] # # ONESHOT test # # Loads folds saved either as `cv_folds.pkl` or as per-fold pickles in a directory named `folds_interaction-type`. Trains an MLP per fold and reports fold-wise metrics and mean ± std. # %% import os os.environ["CUDA_DEVICE_ORDER"]="PCI_BUS_ID" os.environ["CUDA_VISIBLE_DEVICES"]="1" ...
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# %% [markdown] # # Training from CV folds # # Loads folds saved either as `cv_folds.pkl` or as per-fold pickles in a directory named `folds_interaction-type`. Trains an MLP per fold and reports fold-wise metrics and mean ± std. # %% import os os.environ["CUDA_DEVICE_ORDER"]="PCI_BUS_ID" os.environ["CUDA_VISIBLE_DEVI...
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# %% # Import library import glob, json, os, pickle import numpy as np import mne import pandas as pd from mne.viz import plot_topomap import matplotlib.pyplot as plt from sklearn.metrics import confusion_matrix import mat73 import fnmatch import seaborn as sns from collections import Counter from scipy.stats import t...
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# %% [markdown] # # Training from CV folds # # Loads folds saved either as `cv_folds.pkl` or as per-fold pickles in a directory named `folds_interaction-type`. Trains an MLP per fold and reports fold-wise metrics and mean ± std. # %% import os os.environ["CUDA_DEVICE_ORDER"]="PCI_BUS_ID" os.environ["CUDA_VISIBLE_DEVI...
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# %% [markdown] # # Training from CV folds # # Loads folds saved either as `cv_folds.pkl` or as per-fold pickles in a directory named `folds_interaction-type`. Trains an MLP per fold and reports fold-wise metrics and mean ± std. # %% import os os.environ["CUDA_DEVICE_ORDER"]="PCI_BUS_ID" os.environ["CUDA_VISIBLE_DEVI...
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# %% import pandas as pd import numpy as np import os # %% Semi_processed = '/storage/Arushi/090526_EvoAge/kg_formation/processed_data/Monarch/' Processed = '/storage/Arushi/090526_EvoAge/kg_formation/processed_data/Monarch/Monarch_final/' # %% # %% # %% import os import re import numpy as np import pandas as pd ...
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# %% [markdown] # # Monarch KG → Knowledge Graph (KG) Builder # # **Source:** [Monarch Initiative KG](https://monarchinitiative.org/) — # # ## What this notebook does # # 1. Loads all reference dictionaries (NCBI, PubChem, ChEBI, UniProt, DO, MONDO). # 2. Loads the full Monarch KG edge pickle, strips NCBITaxon prefi...
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# %% [markdown] # # imports # %% def wrap_labels(label, max_length=20, ignore=[]): if len(label) > max_length: for i in ignore: if i in label: return label last_space = label.rfind(' ', 0, max_length) if last_space > 0: if len(label[last_space+1:]) > ...
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# %% import sys import warnings warnings.filterwarnings('ignore') import os import pickle import pandas as pd import numpy as np import h5py import os import tqdm from tqdm import tnrange as trange import seaborn as sns import matplotlib as mpl from matplotlib import rcParams import matplotlib.pyplot as plt mpl.rcPar...
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# %% [markdown] # # Training from CV folds # # Loads folds saved either as `cv_folds.pkl` or as per-fold pickles in a directory named `folds_interaction-type`. Trains an MLP per fold and reports fold-wise metrics and mean ± std. # %% import os os.environ["CUDA_DEVICE_ORDER"]="PCI_BUS_ID" os.environ["CUDA_VISIBLE_DEVI...
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# %% import os import sys # Get the absolute path of the current notebook's directory notebook_dir = os.getcwd() parent_dir = os.path.abspath(os.path.join(notebook_dir, "..")) sys.path.append(parent_dir) # Add parent directory to sys.path # model import torch import torch.nn as nn import torch.nn.functional as F impo...
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# %% import os import sys # Get the absolute path of the current notebook's directory notebook_dir = os.getcwd() parent_dir = os.path.abspath(os.path.join(notebook_dir, "..")) sys.path.append(parent_dir) # Add parent directory to sys.path # model import torch import torch.nn as nn import torch.nn.functional as F impo...
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# %% [markdown] # # [Amygdala GABA Neurons: Gatekeepers of Stress and Reproduction in Female Mice ](https://www.biorxiv.org/content/10.1101/2025.01.06.631361v4). Analysis pipeline + Figures # %% [markdown] # # 🧰 Preparation Block for Analysis # %% # Check the current Python version for a stable connection !python --...
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# %% import os import sys # Get the absolute path of the current notebook's directory notebook_dir = os.getcwd() parent_dir = os.path.abspath(os.path.join(notebook_dir, "..")) sys.path.append(parent_dir) # Add parent directory to sys.path # model import torch import torch.nn as nn import torch.nn.functional as F impo...
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# %% import os import pydicom import numpy as np import matplotlib.pyplot as plt # %% import nibabel as nib import numpy as np import os # Parameters case_name = "L067" nifti_path = f"/mnt/nas7/data/maria/final_features/nifti_new_dataset/{case_name}_volume_hu2.nii" center = np.array([505, 247, 125]) radius_mm = 15....
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# %% import os from datetime import datetime import numpy as np import pandas as pd import scipy.stats as stats import statsmodels.formula.api as smf # Local module imports from helper_analysis import ( load_experiment_data, summarize_data, load_probe_data, map_cluster_depths_to_real_dimensions, no...
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# %% import os from datetime import datetime import numpy as np import pandas as pd import scipy.stats as stats import statsmodels.formula.api as smf # Local module imports from helper_analysis import ( load_experiment_data, summarize_data, load_probe_data, map_cluster_depths_to_real_dimensions, no...
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# %% import os from datetime import datetime import numpy as np import pandas as pd import scipy.stats as stats import statsmodels.formula.api as smf # Local module imports from helper_analysis import ( load_experiment_data, summarize_data, load_probe_data, map_cluster_depths_to_real_dimensions, no...
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# %% [markdown] # # This notebook will analyze raw spike data from recorded sessions in the experiments outlined in Rolon-Martinez, et. al (2024). # %% [markdown] # ## Functions and Plotting Parameters # %% [markdown] # ### Import packages you will need for running this script ## # %% import os import numpy as np im...
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# %% [markdown] # # Cytocraft's performance on Platforms # %% [markdown] # ## imports # %% import pickle, copy, importlib, math, os import seaborn as sns import numpy as np import pandas as pd from tqdm import tqdm import warnings warnings.simplefilter(action='ignore', category=FutureWarning) from cytocraft.craft imp...
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# %% [markdown] # # This notebook will analyze raw spike data from recorded sessions in the experiments outlined in Rolon-Martinez, et. al (2024). # %% [markdown] # ## Functions and Plotting Parameters # %% [markdown] # ### Import packages you will need for running this script ## # %% import os import numpy as np im...
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# %% [markdown] # # This notebook will analyze raw spike data from recorded sessions in the experiments outlined in Rolon-Martinez, et. al (2024). # %% [markdown] # ## Functions and Plotting Parameters # %% [markdown] # ### Import packages you will need for running this script ## # %% import os import numpy as np im...
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# %% [markdown] # # Cytocraft Analysis Notebook - Reproducibility # # This notebook contains the downstream analysis code for the cytocraft project. # # ## Data Requirements # Before running this notebook, please ensure you have downloaded the required datasets and placed them in the appropriate directories: # # - `...
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# %% import pandas as pd # %% [markdown] # ## Main Figure 1 # %% [markdown] # ## 1b # %% """ EvoAge KG — Figure 1b: single-ring sunburst/donut of data sources, wedge size = log10(Total edges), colored by KG_Type category. Reads figure1b.csv (columns: Source, KG_Type, Total, log) and reproduces evoage_sunburst_1b.sv...
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###NODDI-GBSS License NODDI-GBSS (c) by Arash Nazeri, Jon Pipitone, and Tina Roostaei Kimel Family Translational Imaging-Genetics Research Lab. NODDI-GBSS is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License. You should have received a copy of the license along with this work. If ...
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Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) Copyright (c) 2026 Laboratory of Cheminformatics (LCi), Faculty of pharmacy, Federal University of Goiás, Brazil. This work is licensed under the Creative Commons Attribution-NonCommercial 4.0 International License. To view a copy of this lic...
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Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) Copyright (c) 2025 Laboratory of Cheminformatics (LCi), Faculty of pharmacy, Federal University of Goiás, Brazil. This work is licensed under the Creative Commons Attribution-NonCommercial 4.0 International License. To view a copy of this lic...
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Copyright (c) 2005-2016 Galaxy Contributors (see https://github.com/galaxyproject/galaxy/blob/dev/CONTRIBUTORS.md) Du Novo is licensed under GPLv2 (see the file "COPYING"). The files "swalign.c" and "swalign.h" contain software copyrighted by Nicolaus Lance Hepler and released under the MIT license, which can be foun...
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MIT License Copyright (c) 2026 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, subli...
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Copyright 2020-2021 Tao Cui, Tingting Wang Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, ...
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Copyright 2020-2023 Tao Cui, Tingting Wang Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, ...
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Copyright 2020-2024 Tao Cui, Tingting Wang Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, ...
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Creative Commons Attribution-ShareAlike 4.0 International Creative Commons Corporation ("Creative Commons") is not a law firm and does not provide legal services or legal advice. Distribution of Creative Commons public licenses does not create a lawyer-client or other relationship. Creative Commons makes its licenses ...
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Copyright 2022 Robyn Speer Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distri...
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Copyright 2020 Scott Prahl 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...
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MIT License Copyright (c) 2025 [Liping Fu] Permission is hereby granted, free of charge, to any person obtaining a copy of this Brain Atlas - FDG and associated documentation files (the "Atlas"), to deal in the Atlas without restriction, including without limitation the rights to use, copy, modify, merge, publish, di...
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MIT License Copyright (c) 2021 Adam 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, ...
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MIT License Copyright (c) 2024 wobc 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, ...
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MIT License Copyright (c) 2024 PyFox 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,...
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MIT License Copyright (c) 2024 Binxu 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,...
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MIT License Copyright (c) 2024 paran 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,...
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MIT License Copyright (c) 2026 Ellen 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,...
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MIT License Copyright (c) 2021 OpenMM 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...
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MIT License Copyright (c) 2024 JBauer 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...
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MIT License Copyright (c) 2022 pressm 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...
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MIT License Copyright (c) 2021 QA4IQI 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...
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MIT License Copyright (c) 2025 mirivar 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, distribut...
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MIT License Copyright (c) 2025 WeiYang 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, distribut...
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MIT License Copyright (c) 2025 Zeyu Fu 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, distribut...
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MIT License Copyright (c) 2025 leboero 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, distribut...
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MIT License Copyright (c) 2025 Lin Cai 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, distribut...
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MIT License Copyright (c) 2026 Jie Lin 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, distribut...
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MIT License Copyright (c) 2018 Tian Ge 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, distribut...
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AU License Copyright (c) 2025 Chao Sun 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, distribut...
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MIT License Copyright (c) 2025 Xiang Li 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, distribu...
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MIT License Copyright (c) 2022 Xuan Kan 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, distribu...
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MIT License Copyright (c) 2025 Guan Lab 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, distribu...
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MIT License Copyright (c) 2017 XenderLiu 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, distrib...
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MIT License Copyright (c) 2026 云抒语 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, s...
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MIT License Copyright (c) 2026 dbheadley 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, distrib...
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MIT License Copyright (c) 2026 Ahuja Lab 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, distrib...
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MIT License Copyright (c) 2021 Göke Lab 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, distribu...
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MIT License Copyright (c) 2024 Shujun-He 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, distrib...
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MIT License Copyright (c) 2026 nikolakoe 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, distrib...
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MIT License Copyright (c) 2018 ALMA ANDERSSON 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, dist...
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MIT License Copyright (c) 2025 Ezio660914 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, distri...
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Copyright (c) 2026 Christopher T. Boughter 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, distri...
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MIT License Copyright (c) 2025 mabelzunce 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, distri...
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MIT License Copyright (c) 2022 Goodman Lab 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, distr...
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MIT License Copyright (c) 2025 AlexDReyes 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, distri...
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MIT License Copyright (c) 2025 CharLamp10 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, distri...
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MIT License Copyright (c) 2025 Jinxin Liu 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, distri...
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MIT License Copyright (c) 2024 Du Jinhong 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, distri...
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MIT License Copyright (c) 2026 amrabozeid 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, distri...
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MIT License Copyright (c) 2026 Reza Pousti 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, distr...
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MIT License Copyright (c) 2025 cbi-bioinfo 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, distr...
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MIT License Copyright (c) 2016 Machens Lab 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, distr...
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MIT License Copyright (c) 2024 Gina Faraci 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, distr...