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09b945d4d2da8dd28ba9a309c0b3fa87fb33fb5bab444c53cef334e2aa125be7
Python
99,292
2,518
import base64 import collections import errno import io import json import logging import mmap import multiprocessing import os import shutil import signal import socket import subprocess import sys import threading import time from functools import cache from pathlib import Path from typing import IO, AnyStr, List, Op...
e1cc74b2bb1fd75cdf2e37c07bb86ced58ad384a0ed541ecc36b8e38e9e13762
Python
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# based on : https://github.com/theislab/scvelo/blob/1805ab4a72d3f34496f0ef246500a159f619d3a2/scvelo/plotting/velocity_embedding_grid.py#L27 import numpy as np from sklearn.neighbors import NearestNeighbors from datetime import datetime from scipy.stats import norm as normal from typing import Union from scipy.spatial ...
4950d7181b95391e3dc9300fe022ff52c02e0aebb39491189275de62b9a98039
Python
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import mozaik from mozaik.controller import Global from mozaik.experiments import Experiment from parameters import ParameterSet import mozaik.stimuli.vision.topographica_based as topo import mozaik.stimuli.vision.visual_stimulus as vs import numpy from mozaik.stimuli import InternalStimulus from mozaik.tools.distribut...
d2e44939816d8dc273ab41f87561411665eb894b8e7e2e2dc5f09e9e18faa708
Python
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# tensor_generators.py # # On-the-fly data generation of tensors for training or prediction. # # October 2018 # Sam Friedman # sam@broadinstitute.org # Python 2/3 friendly from __future__ import print_function # Imports import os import csv import copy import math import h5py import time import logging import traceba...
e6acd5218304e45f13b84843e049e3077b03b0e8547372188bfb97c2b6e9b07a
Python
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from __future__ import annotations from scanpy import read_10x_h5 from scanpy import logging as logg import json from pathlib import Path, PurePath from typing import BinaryIO, Literal import pandas as pd from matplotlib.image import imread from typing import Tuple, Optional, Literal, Dict import numpy as np from sci...
758845a94bc97970ba726f692a3f45821f577c0105a70db489f3ddb2df6433f2
Python
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# TensorMaps automatically generated by tensor_map_maker.py # DO NOT EDIT from ml4h.defines import StorageType from ml4h.metrics import weighted_crossentropy from ml4h.tensormap.ukb.demographics import prevalent_incident_tensor from ml4h.TensorMap import TensorMap, Interpretation, make_range_validator # TensorMaps...
2ca43ede8e2bc559f1b11ed4431574c0ce6877a12e38e4467ac472f4c3f1d14d
Python
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""" Copyright (c) Meta Platforms, Inc. and affiliates. This source code is licensed under the MIT license found in the LICENSE file in the root directory of this source tree. Original CGCNN k-hot elemental embeddings. """ from __future__ import annotations KHOT_EMBEDDINGS = { 1: [ 0, 1, ...
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Python
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MANUAL_CELL_MATCHES = { ('2018-08-07-5', 'data000'): '''#ON parasol 341:data001,1174;data002,1004 421:data001,18;data002,467 1114:data001,1052,1044;data002,1049 1032:data001,614;data002,1023 704:data001,396;data002,1085,1016 79:data001,532;data002,777 880:data001,381;data002,943 182:data001,1051;data002,593...
b61330d564c2a915828cbd21354a874da26e86353fa1ac8f935fe03dc86fadcb
Python
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from typing import Dict, List, Tuple import torch import torch.nn as nn import torch.nn.functional as F from lpips import LPIPS from numpy import fromfunction from torch.fft import fftn from torch.nn.modules.loss import _Loss from pytorch_msssim import SSIM, MS_SSIM from src.handlers.general import TBSummaryTypes from...
5fd5c37139f41ad76d86a524c1645bba874b94dc16e5b43c42689d9ded6669f6
Python
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""" UCE model implementation for omicverse. This module provides a wrapper for the UCE (Universal Cell Embeddings) model, following the exact logic of the original eval_single_anndata.py script. """ import os import tempfile import pickle import numpy as np import pandas as pd import torch import torch.nn as nn from ...
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Python
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# -*- coding: utf-8 -*- # Form implementation generated from reading ui file 'basic_form_pending.ui' # # Created by: PyQt5 UI code generator 5.15.2 # # WARNING: Any manual changes made to this file will be lost when pyuic5 is # run again. Do not edit this file unless you know what you are doing. from PyQt5 import Q...
63bf28ed41dc01cea123a8ddcaadb89a921a5f3c60d3fe9f13607b7bd115e449
Python
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""" Copy from pegasus and cellual """ from typing import Union, Tuple, Optional, Sequence, List, Dict import anndata import numpy as np import pandas as pd import skmisc.loess as sl import scanpy as sc import time import warnings from scipy.sparse import issparse, csr_matrix from ..utils import load_signatures_fro...
ae0de02df64a8ccc3f370fd31af3280d533f538bfb5d7f10775679fc50f4b876
Python
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# -*- coding: utf-8 -*- # Form implementation generated from reading ui file 'auto_form.ui' # # Created by: PyQt5 UI code generator 5.15.2 # # WARNING: Any manual changes made to this file will be lost when pyuic5 is # run again. Do not edit this file unless you know what you are doing. from PyQt5 import QtCore, Qt...
42aba69f78014b3bd455b6ffe0190b51a09b8aa5e8a317b300b811eb753f79d2
Python
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# -*- coding: utf-8 -*- # Form implementation generated from reading ui file 'auto_form.ui' # # Created by: PyQt5 UI code generator 5.15.2 # # WARNING: Any manual changes made to this file will be lost when pyuic5 is # run again. Do not edit this file unless you know what you are doing. from PyQt5 import QtCore, Qt...
f4d8382424ac3470f0605eb6735a09ac4666595249c4b8c286b4aa91b3eefad2
Python
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# Partially based on codebase by Leland McInnes (https://github.com/lmcinnes/umap) from __future__ import print_function import numpy as np import numba import scipy from scipy.optimize import curve_fit from sklearn.neighbors import KDTree from sklearn.metrics import pairwise_distances import warnings #INT32_MI...
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Python
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""" Copy from pegasus and cellual """ import os import logging from functools import reduce from random import seed, sample from typing import Union, Optional, Sequence, Tuple, List, Dict import pandas as pd import anndata import numpy as np import matplotlib.pyplot as plt from scipy import sparse from matplotlib....
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Python
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import numpy as np import matplotlib.pyplot as plt import matplotlib.gridspec as gridspec import sklearn.decomposition as skd import sklearn.manifold as skm import sklearn.linear_model as sklm import sklearn.svm as sk_svm import scipy.stats as sts import arviz as az import itertools as it import seaborn as sns import f...
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Python
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"""Neural net base class This is the most flexible class, not making assumptions on the kind of task being performed. Subclass this to create more specialized and sklearn-conforming classes like NeuralNetClassifier. """ import fnmatch from collections.abc import Mapping from functools import partial from itertools i...
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Python
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# Copyright (C) 2019-2022 Intel Corporation # Copyright (C) CVAT.ai Corporation # # SPDX-License-Identifier: MIT from __future__ import annotations import os.path as osp import re import sys from collections import defaultdict from collections.abc import Callable, Collection, Generator, Iterable, Iterator, Mapping, S...
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Python
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"""Trajectory visualizations shared by trajectory inference backends.""" from __future__ import annotations from dataclasses import dataclass from typing import Optional import warnings import numpy as np import pandas as pd import matplotlib.pyplot as plt import matplotlib.colors as mcolors import matplotlib.pathef...
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Python
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# -*- coding: utf-8 -*- # Form implementation generated from reading ui file 'basic_form.ui' # # Created by: PyQt5 UI code generator 5.15.2 # # WARNING: Any manual changes made to this file will be lost when pyuic5 is # run again. Do not edit this file unless you know what you are doing. from PyQt5 import QtCore, Q...
c562601f0ed72b55e3e1f3e4acfd6289c0be8e624baf6338cf82ff8d1998293e
Python
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'''This module implements the essential components of a microscopy setup. By assembling an excitation beam, a STED beam, a detector, and fluorescence molecules, to obtain a microscope setup. The following code gives an example of how to create such setup and use it to measure and plot the detected signal given some ``...
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Python
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# Copyright 2023 Google LLC # # 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 # # https://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, ...
163f079c8226722533d324bf75e512087775460a4ef02471c121f07fb83a8e1b
Python
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# # \file generator.py # # \brief Generates the CUTLASS Library's instances # import enum import os.path import shutil import argparse from library import * from manifest import * ################################################################################################### # def CudaToolkitVers...
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Python
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from collections.abc import Mapping import matplotlib.pyplot as plt import numpy as np import pandas as pd import seaborn as sns from anndata import AnnData from matplotlib import cm from matplotlib.colors import Normalize, TwoSlopeNorm, to_hex from matplotlib.text import Text from pandas.api.types import CategoricalD...
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Python
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# Copyright (C) CVAT.ai Corporation # # SPDX-License-Identifier: MIT import gzip import io import json import math import os import os.path as osp import zipfile from collections import Counter from collections.abc import Iterable, Sequence from copy import deepcopy from functools import partial from http import HTTPS...
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Python
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"""Pseudotime → terminal-state → lineage-fate unification. Implements the 4-step pipeline shared by MIRA (`mira.pseudotime.*`) and CellRank (`cellrank.kernels.PseudotimeKernel` + `GPCCA`), in pure numpy/scipy with no heavyweight dependencies (no pyGPCCA, no jax): 1. bias kNN graph — Palantir-style hard thr...
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Python
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import os import numpy as np import pickle # import stan # import pystan as ps import arviz as az import scipy.special as spsp import sklearn.manifold as skm import sklearn.model_selection as skms import sklearn.svm as skc import sklearn.linear_model as sklm import sklearn.preprocessing as skp import sklearn.pipeline ...
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Python
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import sys from dataclasses import dataclass from enum import Enum from typing import List, Union, Dict, Tuple, Callable, Optional import numpy as np import rawmovie.load_movie as load_movie import spikebinning from movie_upsampling import compute_interval_overlaps, integer_upsample_movie import visionloader as vl fro...
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Python
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""" scGPT model implementation with simplified interface. """ import copy import json import time import warnings from pathlib import Path from typing import Dict, Any, Optional, Union, List, Tuple import numpy as np import pandas as pd import torch import torch.nn as nn from torch.utils.data import Dataset, DataLoad...
cadda70d677295e7efb64f5864a390dd22745c7a921fe8013b5c9f295151eea6
Python
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import pytest import os import base64 import pathlib import sqlite3 import struct import zlib import hashlib import inspect import json from tabulate import tabulate import numpy as np from collections import defaultdict from candycrunch.prediction import * import candycrunch.utils from glycowork.motif.graph import co...
baf6af1c98405f61b1cc7e0198b27b4e9751a447327c46609df07d340cb5bdc4
Python
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#!/usr/bin/env python import sys import datetime import argparse import json import warnings import textwrap import numpy import scipy import scipy.stats import pandas from matplotlib import pyplot from matplotlib.backends.backend_pdf import PdfPages from sv_utils import common, plotting, genomics_io, pedigree_tools, ...
1b39f8b8bd77cc75db07e4a58b1176ced41db5e5b34e4906004dd6eb54a2bb5a
Python
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import inspect import logging from typing import ( TYPE_CHECKING, Any, Awaitable, Callable, Dict, Generic, List, Literal, Optional, Tuple, TypeVar, Union, overload, ) try: from typing import Never, ParamSpec except ImportError: from typing_extensions import N...
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Python
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#!/usr/bin/env python # -*- coding: utf-8 -*- """ The functions apply_shifts_dft, register_translation, _compute_error, _compute_phasediff, and _upsampled_dft are from SIMA (https://github.com/losonczylab/sima), licensed under the GNU GENERAL PUBLIC LICENSE, Version 2, 1991. These same functions were adapted from sc...
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Python
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import copy import logging import logging.handlers import os import pathlib import random import re import subprocess import urllib import urllib.request from collections import defaultdict from collections.abc import Iterable from enum import Enum from functools import lru_cache from queue import Queue from typing imp...
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Python
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import torch from torch.utils.data import Dataset, DataLoader, SubsetRandomSampler, random_split import pandas as pd import numpy as np import os import random from collections import defaultdict, Counter from itertools import combinations import json import torch.nn as nn import torch.nn.functional as F from sklearn.m...
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Python
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import numpy as np import pandas as pd import os import itertools from scipy.stats import shapiro from scipy.stats import ttest_ind from scipy.stats import ranksums from tqdm import tqdm import pickle import time from mpl_toolkits.axes_grid1.inset_locator import inset_axes from matplotlib.patches import Rectangle #, Pa...
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Python
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# -*- coding: utf-8 -*- """ This module contains the Mozaik analysis interface and implementation of various analysis algorithms For more documentation refer to :doc:`mozaik.analysis` """ import numpy import scipy import scipy.signal import time import quantities as qt import mozaik.tools.units as munits from mozaik.t...
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Python
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#!/usr/bin/env python # ================================ # @auther: Rongbin Zheng # @email: Rongbin.Zheng@childrens.harvard.edu # @date: July 2025 # ================================ import os,sys import time, re import pickle as pk import _pickle as cPickle from datetime import datetime import numpy as np import pand...
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Python
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# recipes.py import json # Imports import os import csv import copy import h5py import glob import logging import datetime import numpy as np import pandas as pd import keras from functools import reduce from google.cloud import storage from timeit import default_timer as timer from collections import Counter, defaul...
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Python
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# MRI-specific tensormaps import csv import logging import os from typing import Dict, Tuple, Callable import h5py import numpy as np from scipy.signal import convolve2d from scipy.ndimage import median_filter from scipy.ndimage.interpolation import rotate import tensorflow as tf from tensorflow.keras.utils import to_...
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Python
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import asyncio import logging import threading import time import traceback import uuid import weakref from collections import defaultdict from contextlib import nullcontext from dataclasses import asdict, dataclass from typing import ( Any, Dict, List, Optional, Set, Tuple, Union, ) import...
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Python
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from mozaik.analysis.analysis import Analysis from mozaik.analysis.data_structures import SingleValue, AnalogSignal, PerNeuronValue from mozaik.analysis.technical import NeuronAnnotationsToPerNeuronValues import numpy as np import numpy import mozaik.tools.units as munits from neo.core.analogsignal import AnalogSignal ...
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Python
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""" Geneformer model implementation for the SCLLM framework. This module provides a wrapper around the Geneformer model for single-cell RNA-seq analysis, including cell classification, embedding extraction, and in silico perturbation experiments. """ import os import json import warnings import pickle from pathlib im...
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Python
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# -*- coding: utf-8 -*- # Form implementation generated from reading ui file '.\isonet_star_0630.ui' # # Created by: PyQt5 UI code generator 5.15.2 # # WARNING: Any manual changes made to this file will be lost when pyuic5 is # run again. Do not edit this file unless you know what you are doing. from PyQt...
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Python
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# plots.py # Imports import os import csv import re import math import h5py import glob import logging import hashlib import operator import warnings from textwrap import wrap from functools import reduce from datetime import datetime from multiprocessing import Pool from itertools import islice, product from collecti...
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Python
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# Copyright 2023 Google LLC # 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 # https://www.apache.org/licenses/LICENSE-2.0 # Unless required by applicable law or agreed to in writing, sof...
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Python
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import atexit import dataclasses import faulthandler import functools import inspect import io import json import logging import os import sys import threading import time import traceback import urllib import warnings from abc import ABCMeta, abstractmethod from collections.abc import Mapping from contextlib import co...
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Python
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# Copyright (C) 2018-2022 Intel Corporation # Copyright (C) CVAT.ai Corporation # # SPDX-License-Identifier: MIT import itertools import os import os.path as osp import re import shutil import textwrap import zlib from abc import ABCMeta, abstractmethod from contextlib import suppress from copy import copy from dateti...
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Python
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import os import sys import time # coding: utf-8 from typing import Dict, List, Optional, Tuple from unittest.mock import patch import pytest import ray from ray.autoscaler.v2.event_logger import AutoscalerEventLogger from ray.autoscaler.v2.scheduler import ( NodeTypeConfig, ResourceDemandScheduler, Reso...
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Python
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# biolgca is a Python package for simulating different kinds of lattice-gas # cellular automata (LGCA) in the biological context. # Copyright (C) 2018-2022 Technische Universität Dresden, contact: simon.syga@tu-dresden.de. # The full license notice is found in the file lgca/__init__.py. """ Abstract base classes. Thes...
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Python
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import numpy as np; np.set_printoptions(precision=2); np.random.seed(0) import torch; torch.set_printoptions(precision=2) import torch.nn as nn import matplotlib.pyplot as plt import matplotlib from matplotlib.font_manager import FontProperties from mpl_toolkits import mplot3d import seaborn as sns import time import...
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Python
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""" Elikopy @author: qdessain, msimon """ import datetime import os import json import math import shutil import time import subprocess import matplotlib.pyplot import matplotlib import elikopy.utils from elikopy.individual_subject_processing import (preproc_solo, dti_solo, white_mask_solo, noddi_solo, diamond_...
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Python
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#!/usr/bin/env python3 # -*- coding: utf-8 -*- # pylint: disable=broad-except # pylint: disable=invalid-name # pylint: disable=line-too-long # pylint: disable=multiple-statements # pylint: disable=too-many-lines #------------------------------------------------------------------------------- ''' This file contains th...
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Python
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import pylab import numpy import mozaik.storage.queries as queries import matplotlib.gridspec as gridspec from mozaik.visualization.plotting import Plotting from mozaik.visualization.helper_functions import * from parameters import ParameterSet from mozaik.storage.queries import * from mozaik.analysis.analysis import ...
1f1bc47d44629c1a9ff81a7a59771217799305fe2cd33ff044c75db4c74eaabd
Python
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import pylab import numpy import mozaik.storage.queries as queries import matplotlib.gridspec as gridspec from mozaik.visualization.plotting import Plotting from mozaik.visualization.helper_functions import * from parameters import ParameterSet from mozaik.storage.queries import * from mozaik.analysis.analysis import ...
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Python
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import pylab import numpy import mozaik.storage.queries as queries import matplotlib.gridspec as gridspec from mozaik.visualization.plotting import Plotting from mozaik.visualization.helper_functions import * from parameters import ParameterSet from mozaik.storage.queries import * from mozaik.analysis.analysis import ...
0fa270b83c230c7c3364769005dc15ed97875f247c94f4cb3ace19fccd862363
Python
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from .bonsai_helpers import * import os from scipy.optimize import fminbound from scipy.spatial import distance import pandas as pd import csv from .bonsai_treeHelpers import Tree, TreeNode, optimiseTStar from . import bonsai_globals as bs_glob import copy import gc import json import heapq import logging FORMAT = '%...
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Python
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import numpy as np import pandas as pd import matplotlib.pyplot as plt import seaborn as sns import math from scipy import sparse import networkx as nx from matplotlib.patches import FancyBboxPatch, ConnectionPatch import matplotlib.patches as mpatches from sklearn.cluster import KMeans from sklearn.metrics.pairwise im...
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Python
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from __future__ import annotations import json import logging import os import pickle import re from pathlib import Path import networkx as nx import numpy as np import pandas as pd from anndata import AnnData from scipy.sparse import csr_matrix from sklearn.metrics.pairwise import cosine_similarity from tqdm import t...
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import pylab import numpy import mozaik.storage.queries as queries import matplotlib.gridspec as gridspec from mozaik.visualization.plotting import Plotting from mozaik.visualization.helper_functions import * from parameters import ParameterSet from mozaik.storage.queries import * from mozaik.analysis.analysis import ...
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# -*- coding: utf-8 -*- """ SASSI Signal Analysis Selection, Segmentation, and Integration formerly BASSPRO Breathing Analysis Selection and Segmentation for Plethysmography and Respiratory Observations *** built as part of the Russell Ray Lab Breathing And Physiology Analysis Pipeline *** Breathe Easy - an automated...
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"""Tests for net.py Although NeuralNetClassifier is used in tests, test only functionality that is general to NeuralNet class. """ import copy from functools import partial import os from pathlib import Path import pickle import re from unittest.mock import Mock from unittest.mock import call from unittest.mock impo...
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# coding: utf-8 # # Table of Contents # # 1. [Import stuff](#import_everything) # 2. [Set whether these analyses are done for this analysis or not](#set_whether_these_analyses_are_done_for_this_analysis_or_not) # 3. [Load data](#os.path.exists_checkpoint_fig_dir__load_data) # 1. [Set values for indexing](#Set_so...
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# coding: utf-8 # # Table of Contents # # 1. [Import stuff](#import_everything) # 2. [Set whether these analyses are done for this analysis or not](#set_whether_these_analyses_are_done_for_this_analysis_or_not) # 3. [Load data](#os.path.exists_checkpoint_fig_dir_load_data) # 1. [Set values for indexing](#Set_som...
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# coding: utf-8 # # Table of Contents # # 1. [Import stuff](#import_everything) # 2. [Set whether these analyses are done for this analysis or not](#set_whether_these_analyses_are_done_for_this_analysis_or_not) # 3. [Load data](#os.path.exists_checkpoint_fig_dir_load_data) # 1. [Set values for indexing](#Set_som...
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#!/usr/bin/env python3 # -*- coding: utf-8 -*- # pylint: disable=broad-except # pylint: disable=invalid-name # pylint: disable=line-too-long # pylint: disable=multiple-statements # pylint: disable=too-many-lines #------------------------------------------------------------------------------- ''' This file contains th...
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import pylab import numpy import pandas import scipy.stats import mozaik.storage.queries as queries import matplotlib.gridspec as gridspec from mozaik.visualization.plotting import Plotting from mozaik.visualization.helper_functions import * from parameters import ParameterSet from mozaik.storage.queries import * from...
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import numpy as np import pandas as pd import scipy from scipy import sparse from scipy.sparse import csr_matrix, csgraph, find from scipy.sparse.csgraph import minimum_spanning_tree, connected_components import igraph as ig import leidenalg import time from datetime import datetime import matplotlib.pyplot as plt imp...
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# -*- coding: utf-8 -*- # Resource object code # # Created by: The Resource Compiler for PyQt5 (Qt v5.15.2) # # WARNING! All changes made in this file will be lost! from PyQt5 import QtCore qt_resource_data = b"\ \x00\x16\x8f\x48\ \x89\ \x50\x4e\x47\x0d\x0a\x1a\x0a\x00\x00\x00\x0d\x49\x48\x44\x52\x00\ \x00\x0f\x47\x...
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from ml4h.defines import StorageType from ml4h.TensorMap import TensorMap, Interpretation categorical_21_completeness_80 = TensorMap( 'categorical_21_completeness_80', Interpretation.CATEGORICAL, shape=(21,), loss='mse', path_prefix='categorical', metrics=[], channel_map={ 'death': 0, 'Pacemaker_No...
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""" Copyright (c) Meta Platforms, Inc. and affiliates. This source code is licensed under the MIT license found in the LICENSE file in the root directory of this source tree. UMA Nitro: a standalone UMA-small model for energy, force, and stress inference. ``UMANitroModel`` is built directly from an inference checkpo...
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import pandas as pd chm13_dict={'closest GENCODE ID': {'CHM13_G0002360': 'None', 'CHM13_G0002906': 'None', 'CHM13_G0003812': 'None', 'CHM13_G0006285': 'None', 'CHM13_G0007830': 'None', 'CHM13_G0008327': 'None', 'CHM13_G0008490': 'None', 'CHM13_G0008583': 'None', 'CHM13_G0011119': 'None', 'CHM13_G0014011': 'None', 'CHM...
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# Copyright (C) 2022 Intel Corporation # Copyright (C) CVAT.ai Corporation # # SPDX-License-Identifier: MIT import io import itertools import json import operator import os import os.path as osp import re import zipfile from collections.abc import Generator, Iterable, Sequence from copy import deepcopy from datetime i...
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import numpy as np from sklearn.neighbors import NearestNeighbors from datetime import datetime from scipy.stats import norm as normal from mpl_toolkits.axes_grid1 import make_axes_locatable from scipy.spatial import distance from scipy.sparse import csr_matrix, csgraph, find import math import pandas as pd import nump...
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# Copyright (C) 2019-2022 Intel Corporation # Copyright (C) CVAT.ai Corporation # # SPDX-License-Identifier: MIT from __future__ import annotations import mimetypes import os import re import shutil import string import textwrap import uuid import warnings from collections import OrderedDict from collections.abc impo...
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import os, platform, glob, sys import itertools os.environ["OMP_NUM_THREADS"] = "1" os.environ["OPENBLAS_NUM_THREADS"] = "1" os.environ["MKL_NUM_THREADS"] = "1" os.environ["VECLIB_MAXIMUM_THREADS"] = "1" os.environ["NUMEXPR_NUM_THREADS"] = "1" import numpy as np import pandas as pd import copy as copy_lib import warnin...
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#!/usr/bin/env python # Created by Daniele Silvestro on 02/03/2012 => pyrate.help@gmail.com import argparse, os,sys, platform, time, csv, glob import random as rand import warnings, importlib import importlib.util import copy as copy_lib import json version= "PyRate" build = "v3.1.3 - 20260823" if platform.system() =...
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##### # Copyright (c) 2011-2025, NVIDIA Corporation. 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...
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#!/usr/bin/env python # # Hi There! # You may be wondering what this giant blob of binary data here is, you might # even be worried that we're up to something nefarious (good for you for being # paranoid!). This is a base85 encoding of a zip file, this zip file contains # an entire copy of pip (version 19.3.1). # # Pip...
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import datetime import os import shutil import json import numpy as np import math import subprocess from elikopy.utils import makedir import functools print = functools.partial(print, flush=True) def preproc_solo(folder_path, p, reslice=False, reslice_addSlice=False, denoising=False, denoising_algorithm="mppca_mr...
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import numpy as np from sklearn.neighbors import NearestNeighbors from datetime import datetime from scipy.stats import norm as normal from mpl_toolkits.axes_grid1 import make_axes_locatable from scipy.spatial import distance from scipy.sparse import csr_matrix, csgraph, find import math import pandas as pd import nump...
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import numpy as np from ml4h.TensorMap import TensorMap, Interpretation from ml4h.normalizer import Standardize continuous_164_completeness_80 = TensorMap( 'continuous_164_completeness_80', Interpretation.CONTINUOUS, shape=(164,), loss='log_cosh', path_prefix='continuous', metrics=[], normalization=Standar...
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""" From https://raw.githubusercontent.com/arneschneuing/DiffSBDD/ """ import numpy as np from rdkit import Chem import torch # ------------------------------------------------------------------------------ # Computational # ------------------------------------------------------------------------------ FLOAT_TYPE = t...
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Python
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from .bonsai_helpers import * from . import bonsai_globals as bs_glob import numpy as np import time from scipy.optimize import brentq, minimize from scipy.spatial import distance from scipy.sparse import csr_array, lil_array import itertools import os import gc from itertools import permutations from .bonsai_approxNN...
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# Copyright (C) 2020-2022 Intel Corporation # Copyright (C) CVAT.ai Corporation # # SPDX-License-Identifier: MIT import copy import io import json import logging import os import random import shutil import tarfile import tempfile import xml.etree.ElementTree as ET import zipfile from collections import defaultdict f...
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import copy import math import os from pathlib import Path import ast import pickle from collections import Counter from functools import lru_cache import re import warnings from itertools import combinations, combinations_with_replacement, permutations, product from operator import neg import bisect import multiproces...
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import ast import bisect import contextvars import copy import hashlib import inspect import os import random import re import pickle import pathlib import sqlite3 import struct import tempfile import zlib from collections import Counter, defaultdict from itertools import combinations_with_replacement, groupby, islice ...
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from __future__ import annotations import re import textwrap import warnings import io from contextlib import nullcontext, redirect_stdout from typing import Mapping, Sequence, Literal import anndata import matplotlib.pyplot as plt import networkx as nx import numpy as np import pandas as pd import seaborn as sns fro...
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"""CandyCrunch desktop app: run CandyCrunch on LC-MS/MS files, inspect and curate its predictions, and annotate spectra with CandyCrumbs""" import ast import contextlib import faulthandler import functools import glob import html import importlib.util import io import itertools import json import linecache import multi...
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from ..utils import pyomic_palette from ..single import get_celltype_marker import numpy as np import pandas as pd from scipy import stats from scipy.sparse import issparse import h5py import anndata from tqdm import tqdm,trange import matplotlib.pyplot as plt import seaborn as sns import scanpy as sc from typing impor...
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import math import requests from time import sleep import numpy as np import pandas as pd import scipy.stats as stats import statistics import sys import warnings from scipy.spatial.distance import pdist, squareform from scipy.cluster.hierarchy import linkage, cut_tree, dendrogram, fcluster from scipy.cluster.hierarchy...
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import pandas as pd import numpy as np import matplotlib.pyplot as plt import seaborn as sns import textwrap from scipy import sparse import networkx as nx from matplotlib.patches import FancyBboxPatch, ConnectionPatch import matplotlib.patches as mpatches from matplotlib import patheffects from sklearn.cluster import ...
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--- title: "Distributions of allele-resolved counts" format: gfm: toc: true editor: source --- ```{r} library(ggplot2) library(dplyr) library(cowplot) library(Matrix) ``` ```{r} hippo1 <- readRDS('results/rctd_hippo_1.rds') hippo2 <- readRDS('results/rctd_hippo_2.rds') hippo3 <- readRDS('results/rctd_hippo_3....
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--- title: MEEGLET format: html: code-fold: true jupyter: python3 bibliography: references.bib --- > Morlet wavelets for M/EEG analysis, [ˈmiːglɪt] This package provides a lean implementation of Morlet wavelets [@morlet_wave_1982] *designed for power-spectral analysis of M/EEG resting-state signals* [@hipp2012l...
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--- title: spASE format: gfm: toc: true --- R package for detecting 2D spatial patterns of allele-specific expression in spatial transcriptomics data while controlling for cell type. Provides functions for estimating, plotting, and testing for significant ASE patterns. This repository also contains the code to ...
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--- title: "Visium and Slide-seq cerebellum, mixtures" format: gfm: toc: true editor: source --- ```{r} library(tibble) library(latex2exp) library(dplyr) library(ggplot2) library(rtracklayer) library(data.table) library(tidyr) library(Matrix) ``` ```{r} # for removing x chromosome genes gencode <- import('resu...
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--- title: "Preprocessing" format: gfm: toc: true editor: source --- This document details the pre-processing steps run before the rest of the analysis scripts, including pointing to which scripts were run to perform each step. # Sample table See code in .qmd document for LaTeX table. \begin{table}[] \begin...
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--- title: "Cell type maps" format: gfm: toc: true editor: source --- ```{r} library(spacexr) library(spASE) library(dplyr) library(tidyr) library(ggplot2) library(reshape2) library(viridis) library(pals) library(rtracklayer) library(ggrepel) library(ggthemes) library(tibble) gencode <- import('results/gencod...
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--- title: "Analyzing 129 and CAST transcripts" format: gfm: toc: true editor: source --- ```{r} library(Biostrings) library(Matrix) library(ggplot2) library(tidyr) library(dplyr) library(tibble) library(DECIPHER) library(stringr) ``` # Load in data ```{r} tx <- readDNAStringSet('../inst/extdata/emase.pooled...