sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
936d9601b470248414764f9d6af7e4a340a737d7ab25b7e801af632ba6da38fc | Python | 53,853 | 1,413 | import os
import json
import pickle
import shutil
import re
from collections import namedtuple
import glob
from typing import Callable, Union
import numpy as np
import mdtraj
import torch
from sam.coords import sample_data
from sam.data.sequences import aa_list, aa_one_letter
# from sam.data.common import (# get_pro... |
18516bdd6bbb36e14a9546770db815fc01a619479254bac2ee95b1f6a9d38519 | Python | 53,861 | 1,053 | # -*- coding: utf-8 -*-
ModulePy = str('NMF_demixing__ProofOfPrinciple_v23_20240617.py')
'''
Description: NMF analysis demixing spatio-temporal ensemble signals from Fiber Photometry ensemble video data (proof-of-principle analysis).
- Input files:
(i) raw_ensemble_video_data.mat [videodat... |
146b6687ca7691018fce958a30c3d739a06a0b5a5cb20555ff939e7ad8850771 | Python | 54,207 | 1,294 | #!/usr/bin/env python3
# pylint: disable=line-too-long
import math
import os
import re
import logging
import multiprocessing as mp
from itertools import product, combinations, chain
from scipy import stats
from scipy.cluster.hierarchy import linkage, cophenet
from scipy.spatial.distance import pdist
import numpy as np
... |
d05dba83623cbfc1b56e169629122f4beb3996dbacedb7517b9e531452c9db6e | Python | 54,250 | 1,342 | # This script is part of pymaid (http://www.github.com/navis-org/pymaid).
# Copyright (C) 2017 Philipp Schlegel
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 ... |
4c9c797d2b15629edf9db64ed77670de720f29b2032280380bf921d0b4dd6ed5 | Python | 54,336 | 1,108 | import simtk.openmm as openmm
import os
import copy
import openmmtools.mcmc as mcmc
import openmmtools.integrators as integrators
import openmmtools.states as states
from openmmtools.states import ThermodynamicState
import numpy as np
import mdtraj as md
import mdtraj.utils as mdtrajutils
import simtk.unit as unit
imp... |
8a52038ceac21076c5a62a4dd4e8131748b5200e0ae2a18bfc4a8daa5d87d16f | Python | 54,461 | 1,618 | import os
import sys
import re
import types
import itertools
import matplotlib.pyplot as plt
import numpy
import scipy.stats
import numpy.ma
from ChipseqReport import *
from cgatReport.Tracker import *
# for trackers_derived_sets and trackers_master
if not os.path.exists("conf.py"):
raise IOError("could not find... |
1eef1ce5e41d6f61b3774b0a9370aac7e3030aa58956730dbdbcfbb6b393ba09 | Python | 54,708 | 1,663 | # -*- coding: utf-8 -*-
"""
Created on Tue Nov 3 13:14:05 2020
@author: Xingyan Liu
====================================================
Functions for downstream biological analysis
"""
import os
from pathlib import Path
from typing import Sequence, Union, Mapping, Optional, Callable
import logging
import numpy a... |
32151701f4d85dba445a9ec15fd639ec76bd6a29e4d2d36c9fb8ac7bfadb82df | Python | 55,466 | 1,538 | # Copyright 2020 DeepMind Technologies Limited.
#
# 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... |
c59ddf4ebe0257b127e2f0aa98eb99180b1924579dedc09db3a043960a56698a | Python | 55,691 | 1,191 | import os
import time
from pathlib import Path
from typing import Dict, Any, Optional, List, Union, Tuple
import numpy as np
import pandas as pd
import suite2p
# todo add type hinting controls for expobj
import matplotlib.pyplot as plt
from imagingplus.main.subcore import CellAnnotations, ImagingData
from suite2p impo... |
491d44ce9dd6151e6b24de2143e3e005df8ea9bc52654bbc997c172236df1fe6 | Python | 55,821 | 1,137 | """
==============================================================
Plot figures - updated version post-rebuttal
===============================================================
"""
# Authors: Marie-Constance Corsi <marie-constance.corsi@inria.fr>
#
# License: BSD (3-clause)
import pandas as pd
import ptitprince as p... |
08a9d4bf0d8fd377305d6ba46c7ee02f80f1bda9bcec953dd49608c783e69074 | Python | 55,860 | 1,681 | """===========================
Pipeline transcriptdiffexpression
===========================
To do: update documentation and pipeline.ini. e.g supports sailfish too!
Overview
========
RNA-Seq differential expression analysis can, broadly speaking, be
performed at two levels. Gene-level and transcript-level.
As trans... |
be6854aa4476dc57767e9a81e516fa5adfbc90b3e2bf88a5f59f644084fc001d | Python | 55,911 | 1,616 | # Copyright 2024 DeepMind Technologies Limited
#
# AlphaFold 3 source code is 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... |
821e6973d9c322b8ee0851a03fe0a99c0030f4b8343195c40015caef1a6bd4b5 | Python | 55,965 | 1,264 | import numpy as np
import torch
import scipy
import matplotlib.pyplot as plt
from scipy.stats import rv_discrete
def set_task_defaults(task_params, task='sequential'):
"""
Sets defaults for stimulus change task
"""
if 'noise_type' not in task_params: task_params['noise_type'] = None
if 'noise_scale' not in tas... |
df49489b38313719e32f45545d4286b6011e77cb71df1f5ecb2529e9cbbe6d4d | Python | 56,048 | 1,299 | import torch
# import torch.nn as nn
# from torch.nn import functional as F
import numpy as np
import datetime
from scipy.stats import pearsonr
import matplotlib.pyplot as plt
'''
def model_train(model,data,optimizer,device,EPOCH,loss_func,alpha=None,beta=None,vbeta=1):
"""
function for training... |
cbd93e7bf32257f055692e84d3cbab3d09a80714651ca1642d6c1cab30b047f8 | Python | 56,454 | 1,476 | #!/usr/bin/env python3
import os
import unittest
import networkx as nx
import numpy as np
import pandas as pd
from skbase.utils.dependencies import _check_soft_dependencies
import pgmpy.tests.help_functions as hf
from pgmpy.base import ADMG, DAG
from pgmpy.ci_tests import Pearsonr
from pgmpy.example_models import lo... |
215a010b95bf0754d156b13240ea4d114124834c2186a720a30797cb45999cd1 | Python | 56,488 | 1,565 | """Base interface for traditional large language models (LLMs) to expose.
These are traditionally older models (newer models generally are chat models).
"""
from __future__ import annotations
import asyncio
import builtins
import functools
import json
import logging
from abc import ABC, abstractmethod
from collectio... |
2271cefcea253e1ce650e321d0a7837f88fa85520caface6b3ae26993926942c | Python | 56,799 | 1,288 | import os
import re
import io
import sys
import math
import urllib
import tempfile
import collections
import numpy as np
import matplotlib
import matplotlib.pyplot as plt
import matplotlib.path as mpath
import matplotlib.patches as mpatches
from Bio import SeqIO
import Bio
matplotlib.rcParams["figure.max_open_war... |
fbe69ba0bce0b3bb700638d9a4fb918f201ca285eb277589651169066aaa425e | Python | 57,414 | 1,315 | # New matplotlib colormaps by Nathaniel J. Smith, Stefan van der Walt,
# and (in the case of viridis) Eric Firing.
#
# This file and the colormaps in it are released under the CC0 license /
# public domain dedication. We would appreciate credit if you use or
# redistribute these colormaps, but do not impose any legal r... |
4b5cbae1d0fdf96559a261cef9fdb8f4662d3f83929692d10874fd6f57a01091 | Python | 57,544 | 1,548 | """A de novo peptide sequencing model."""
import collections
import heapq
import itertools
import logging
import warnings
from typing import Any, Dict, Generator, Iterable, List, Optional, Tuple, Union
import einops
import lightning.pytorch as pl
import numpy as np
import torch
import tqdm
from depthcharge.tokenizers... |
0c8bc86388d73b29ee93da2f41be0164ee32dfea837755af6c25c0a43433f419 | Python | 57,770 | 1,411 | ####################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for d... |
ce6712a27184de523972199e063e9f9e868cd89a508dd55303760d33370d4202 | Python | 57,776 | 1,040 | ##
## Summary Visualizations of Gene Ontology Enrichment with GO-Figure!
##
## Authors: Maarten JMF Reijnders and Robert M Waterhouse
##
## Contact: maarten.reijnders@unil.ch or robert.waterhouse@unil.ch
##
import matplotlib
matplotlib.use('Agg')
import sys
import logging
from datetime import date
from collections imp... |
9f83de626a32759cc5388b50e8e6fea738265bfe7ff7ab80728f0abd43dbf2ca | Python | 57,962 | 1,545 | """
===================
CAPseq pipeline
===================
:Author: David Sims
:Release: $Id: pipeline_capseq.py 2900 2011-05-24 14:38:00Z david $
:Date: |today|
:Tags: Python
The CAPseq pipeline imports reads from one or more CAPseq experiments and
performs the following tasks:
* Align reads to the genome usin... |
8f1431ee3afa23cbe1808978c11391a120555210af9ed478489e8edda28eb32c | Python | 58,031 | 1,460 | import torch
from torch import nn
from torch.autograd import Variable
import torch.nn.functional as F
from torch.autograd import Function
from bernn.dl.models.pytorch.utils.stochastic import GaussianSample
from bernn.dl.models.pytorch.utils.distributions import log_normal_standard, log_normal_diag, log_gaussian
from be... |
4e42ea01a481eb1217e71694a54a77bbb33b12eb171ec5a1205cf86e03e17587 | Python | 58,642 | 1,541 | # Copyright Generate Biomedicines, Inc.
#
# 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 ... |
ae9ebbfd13fd106674884065b3d2ff3dddd4b7390bd3a26ca517bc8b7c1f96ea | Python | 59,379 | 1,238 |
import matplotlib
from bernn.utils.pool_metrics import log_pool_metrics
matplotlib.use('Agg')
CUDA_VISIBLE_DEVICES = ""
import uuid
import shutil
import matplotlib.pyplot as plt
import pandas as pd
import numpy as np
import random
import json
import copy
import torch
from itertools import cycle
from torch import nn... |
493f9f1624ba8e07e35f7acaf3aec9c2a443e6d0af7ddd37fcbccde46d976371 | Python | 59,423 | 1,534 | from typing import Set, Dict, List
import lark
from .combinators import *
from .derivation import *
from .categories import *
from .visualization import escape_latex_text
def bwrap(s):
return "(" + s + ")"
def bwrap_tex(s):
return "\\left(" + s + "\\right)"
def is_simple(t):
return isinstance(t, (Skol... |
830e06cab22c3d9e91274ea9cc6aabc846f4db9e1a42867c413cea9b9d763bed | Python | 59,478 | 1,288 | import numpy as np
import pandas as pd
from bed_reader import open_bed
from sklearn.preprocessing import StandardScaler
import multiprocessing as mp
from multiprocessing import Process, Manager
from tqdm import tqdm
from functools import partial
import scipy.stats as stats
from scipy.stats import norm
import matplotli... |
f921c2943f121b877d0d6ab07f191096018dc65f6a6cfaa27f6243d6ca071783 | Python | 59,686 | 1,924 | #!/usr/bin/env python
# coding: utf-8
### Model with simplified training procedure ###
# # Neural network
#
# In this notebook we set up the neural networks with VAMPNet scoring functions and train them for different output sizes and estimate errors by bootstrap aggregation. This notebook can be used with `papermill... |
0c3671135d4ff42ae7a5c177aa430ade66482d42407fc603dfb941dd2a339957 | Python | 59,846 | 1,381 | import math, itertools
import torch
from torch import nn
from torch.utils.data import TensorDataset
import torch.nn.functional as F
import numpy as np
import scipy.special as sps
from plotting import plot_W, plot_B
from net_utils import StatefulBase, Synapse, check_dims, random_weight_init, \
... |
5258655b84413b9a6029aae92adf87a3313c1ca694a68d1d7ef6a91a25099a4a | Python | 59,897 | 1,380 | import numpy as numx
from scipy.signal import convolve2d
import pydeep.base.numpyextension as numxExt
from pydeep.base.activationfunction import Sigmoid
class Weight_layer(object):
''' This class implements a weight layer that connects one unit
layer to another.
'''
@classmethod
def ge... |
c4dd4dffedfaf603401881b1c83da612ab437ac6a94d424ba3be706c39b15fe2 | Python | 60,197 | 1,439 | ####################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for d... |
822dfa2a2ba12749a4c561f8a8fc781c32cb39d54e4bc9e13a92162183bed648 | Python | 60,290 | 1,184 | import yaml
import numpy as np
import pickle
import os
import sys
import simtk.unit as unit
import logging
import warnings
from pathlib import Path
from perses.annihilation.relative import HybridTopologyFactory, RESTCapableHybridTopologyFactory
from perses.app.relative_setup import RelativeFEPSetup
from perses.annihil... |
bc56d65434f4b0429d6c35b17e8936236157ff83500a17d7b2be258229fd0444 | Python | 60,317 | 1,346 | @Created by Bioelectronics Lab (2021-2022)
class Recording:
"""Class for pre-processing and extracting spikes and HR from electroneurograms (ENG)"""
def __init__(self, neural, fs, length, map_array, filename, column_ch):
"""Constructor of neurogram object.
Takes parameters from classmethod open_record, an... |
a6fb407592e86912aa4ce424d180ad23702984b5af7e17cd3bf33839e358c0e9 | Python | 60,442 | 1,430 | """
Parameter assignment tools for the SMIRNOFF (SMIRKS Native Open Force Field) format.
.. codeauthor:: John D. Chodera <john.chodera@choderalab.org>
.. codeauthor:: David L. Mobley <dmobley@mobleylab.org>
.. codeauthor:: Peter K. Eastman <peastman@stanford.edu>
.. todo ::
* Speed up overall import time by putti... |
480dd32e744989acf31ef35bddc91ceb8aa3a5874c88e92c86ad83b8765a1bd6 | Python | 60,460 | 1,389 | """ Module for OmicScope Object Visualization
This module allows the user to extract and visualize information from OmicScope object.
Here, it is possible to evaluate data normalization (MA-Plot, Volcano Plot, Dynamic range plot),
individual protein abundance (barplot, boxplot), search for protein-protein interactions... |
375941f99de9ff97b4d84e8ba6e8eec270fd59bff02c561f06bfc6af8e9990f3 | Python | 60,677 | 1,247 | #!/usr/bin/python3
import matplotlib
from bernn.utils.pool_metrics import log_pool_metrics
matplotlib.use('Agg')
CUDA_VISIBLE_DEVICES = ""
import uuid
import shutil
import matplotlib.pyplot as plt
import pandas as pd
import numpy as np
import random
import json
import copy
import torch
from torch import nn
import o... |
48ad7d7af9b8c58b97d162ec753f3529b97dfa1a8b39a58f2e859517086464e4 | Python | 60,722 | 1,457 | ####################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for detai... |
13e262d17ce21e6698c0875b5b6c90c8688f247de77993023811c440dfebeab3 | Python | 60,938 | 1,033 | import numpy as np
import pandas as pd
from bernn.utils.utils import get_unique_labels
from sklearn.model_selection import StratifiedGroupKFold, StratifiedKFold
from dataset import MSCSV, MS2CSV, MSImages
import multiprocessing
import random
def get_alzheimer(path, args, seed=42):
"""
Args:
path: Path ... |
6ed9d2b23a542c48ac36086af0862548c5568c1cd574b4ca05185a3b162dfdfd | Python | 61,036 | 1,701 | from abc import ABC, abstractmethod
from functools import reduce
from operator import mul
from typing import Iterable, Optional, Union
import torch
class Nodes(torch.nn.Module):
# language=rst
"""
Abstract base class for groups of neurons.
"""
def __init__(
self,
n: Optional[int]... |
bb28689be1f00db10a55465cd4ecd6cf6fd244e979312bef29cfc733bc2571e3 | Python | 61,148 | 1,598 | # Copyright Generate Biomedicines, Inc.
#
# 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 ... |
fb5fa7085012a1304ae952b67dca5d552d6d42944dcd50ca1e4714ed0c0378bd | Python | 61,291 | 1,705 | """Tests for `stream_events(version="v3")` (sync + async) and `ChatModelStream`."""
from __future__ import annotations
import asyncio
import contextlib
import json
from types import SimpleNamespace
from typing import TYPE_CHECKING, Any
import pytest
from langchain_protocol.protocol import (
ContentBlockDeltaData... |
bd6d6d2addbce04cb859210bab429c82bdbe0fb83aa6d985af026b6eb65d6eef | Python | 61,558 | 1,795 | """Tests for the compat bridge (chunk-to-event conversion)."""
from collections.abc import AsyncIterator
from typing import TYPE_CHECKING, Any, cast
import pytest
from langchain_tests.utils.stream_lifecycle import assert_valid_event_stream
from langchain_core.language_models._compat_bridge import (
CompatBlock,
... |
436f4bdadb901388ce3f90403c0edbd9fed55e5ab4996d0676c353659229f39e | Python | 61,661 | 1,764 | """Utilities for running language models or Chains over datasets."""
from __future__ import annotations
import concurrent.futures
import dataclasses
import functools
import inspect
import logging
import re
import unicodedata
import uuid
from collections.abc import Callable
from datetime import datetime, timezone
from... |
198573594621da93addea8f5f11a0d5b398dd5461026c9d19b596fd2f78424b9 | Python | 62,104 | 1,216 | import yaml
import numpy as np
import pickle
import os
import sys
import simtk.unit as unit
import logging
import warnings
from cloudpathlib import AnyPath
from pathlib import Path
from perses.annihilation.relative import HybridTopologyFactory, RESTCapableHybridTopologyFactory
from perses.app.relative_setup import Rel... |
be0194320532c713852fa425b8b75c4d6101a473a25549356a471541c50eda97 | Python | 62,109 | 1,652 | #!/usr/bin/env python
import io
import xml.etree.ElementTree as etree
import pytest
from skbase.utils.dependencies import _check_soft_dependencies
from pgmpy import config
from pgmpy.readwrite import PomdpXReader, PomdpXWriter
@pytest.fixture(params=["numpy", "torch"])
def backend(request):
if request.param ==... |
d4e174622cf22ca58186a50c6f836f6160099f232e58a15caf046fb97dec4d4a | Python | 62,133 | 1,792 | """Chain that takes in an input and produces an action and action input."""
from __future__ import annotations
import asyncio
import builtins
import contextlib
import json
import logging
import time
from abc import abstractmethod
from collections.abc import AsyncIterator, Callable, Iterator, Sequence
from pathlib imp... |
ed1240c42208a30b3e4105c45d9f7b41d8f26de034ef667e721eff48e5ca9b1a | Python | 62,329 | 1,315 | """
SegClassif dock widget module
"""
import functools
import os
import pickle
import random
from typing import Any
import cv2
import matplotlib.pyplot as plt
from napari_plugin_engine import napari_hook_implementation
from napari.utils.notifications import show_info, notification_manager
import time
import numpy as ... |
5d570e2c7a701f5625d8b1a2571a32bb1d166b0dc2d645af8b21dca85056de4b | Python | 62,780 | 1,883 | # Copyright 2021 AlQuraishi Laboratory
# Copyright 2021 DeepMind Technologies Limited
#
# 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
#
# U... |
b0db95c47de85c2126567f62b95d54da380d1869ce82acacd23aa9ef9233296a | Python | 62,802 | 1,363 | from __future__ import print_function
import json, time, os, sys, glob
import shutil
import numpy as np
import torch
from torch import optim
from torch.utils.data import DataLoader
from torch.utils.data.dataset import random_split, Subset
import copy
import torch.nn as nn
import torch.nn.functional as F
import random
... |
64f795fc00d560cd85ef8bbe05412c35439654aa5fd86e4ccdaaab155ad46e21 | Python | 63,016 | 1,070 | from perses.dispersed.utils import *
from openmmtools.states import ThermodynamicState, CompoundThermodynamicState, SamplerState
import numpy as np
import mdtraj as md
import simtk.unit as unit
import logging
import time
from collections import namedtuple
from perses.annihilation.lambda_protocol import LambdaProtocol
... |
3543496ce3a40cb056f4295e7834655f019ed37153ac9af46313ea9a8f71d085 | Python | 63,027 | 1,069 | from perses.dispersed.utils import *
from openmmtools.states import ThermodynamicState, CompoundThermodynamicState, SamplerState
import numpy as np
import mdtraj as md
import simtk.unit as unit
import logging
import time
from collections import namedtuple
from perses.annihilation.lambda_protocol import LambdaProtocol
... |
1835d9682fbb86b7f3d018d1337c48559b7f240acb1f583ebc7234fcc2d02b1d | Python | 63,070 | 1,756 | """=========================================================
pipeline_peakcalling - Produce Peaklist from Bam Files
=========================================================
Overview
========
The aim of this pipeline is to create peaklists in :term:`bed` files from
aligned reads in :term:`bam` files that can then be ... |
11ad86020f729a268ce1b1a351414210c86b8f65253f47ecad088bc884ffb9f8 | Python | 63,423 | 1,454 | from scipy.signal import convolve2d
import model as MODEL
import pydeep.preprocessing as PRE
#from unit_layers import *
class Weight_layer(object):
''' This class implements a weight layer that connects one unit
layer to another.
'''
@classmethod
def generate_2D_connection_matrix(cls... |
74c8f9b7553422a7a0bbd705874844ee103c8926c2c96f154a87e0b824071e1b | Python | 63,491 | 1,383 | from __future__ import print_function
import json, time, os, sys, glob
import shutil
import numpy as np
import torch
from torch import optim
from torch.utils.data import DataLoader
from torch.utils.data.dataset import random_split, Subset
import copy
import torch.nn as nn
import torch.nn.functional as F
import random
... |
2ec1b2811a6005c928b57ddf286173cf32b7c305a62d2fe7fa5443b4f112e5f7 | Python | 64,710 | 1,590 | """Per-message streaming objects for content-block protocol events.
`ChatModelStream` is the synchronous variant returned by
`BaseChatModel.stream_events(version="v3")`. `AsyncChatModelStream` is the
asynchronous variant returned by `BaseChatModel.astream_events(version="v3")`.
Both expose typed projection propertie... |
faf42a68aeea7f73595022f39f7720a7270a45564ccdf579f52886f331e8c21b | Python | 65,631 | 1,359 | """upload / templates / analyze / status / results / export / bundle endpoints.
just a thin wrapper around craniumpy_core.pipeline - no actual algorithm code
should live in here, just request/response stuff and the async job plumbing
(see api/sessions.py).
"""
from __future__ import annotations
import io
from pathli... |
f6bdd9ea26461ed2379210b3f7b9bb7419d1b38f7878f51bc4b71974779f856a | Python | 65,779 | 1,900 | """=====================
Peak calling pipeline
=====================
:Author: Andreas Heger
:Release: $Id$
:Date: |today|
:Tags: Python
The peak calling pipeline applies various peak calling algorithms
on mapped reads.
Overview
========
pipeline_peakcalling takes as input reads aligned to genomic sequence
as :term:... |
7dd90d6473a5e1aec0aeb50dbf5da220cf54585da4704b52152cf8d4f3b6d65d | Python | 66,128 | 1,338 | # network structure
import math
from itertools import cycle
import numpy as np
import ot
import scanpy as sc
import scipy
import scipy.sparse as sp
import torch
import torch.nn.functional as F
from easydl import AccuracyCounter, clear_output, one_hot, variable_to_numpy
from scipy.stats import f, norm, ttest_ind
from t... |
f9074144551b36615aaa18cd61e911d4d1b732bd7c77a08fe3bbfeb062f22aff | Python | 66,236 | 1,687 | #!/usr/bin/env python3
from __future__ import annotations
import itertools
from collections import defaultdict
from collections.abc import Hashable, Iterable
from functools import reduce
from operator import mul
from typing import (
Any,
)
import networkx as nx
import numpy as np
import pandas as pd
from joblib i... |
b1a5db6005abfd6090bacf80869e5776ba1415489d2b33216f7aeb2f13a400f3 | Python | 66,266 | 1,747 | """
Utilities for testing.
"""
import collections
import copy
import functools
import importlib
import itertools
import os
import pathlib
import pprint
import textwrap
from contextlib import contextmanager
import numpy as np
import openmm
import pytest
from openff.units.openmm import to_openmm
from openmm import uni... |
f78e3179497e3dc29483decb15bdc99462c31a9c334bce1217b22a1344d7b9c3 | Python | 66,413 | 1,487 | import ast
import datetime as dt
import inspect
import logging
import os
import shutil
import time
import warnings
from functools import partial
from pathlib import Path
from typing import Union
import click
import humanize
import numpy as np
import yaml
from colorama import Fore, init as init_colorama
from prettytabl... |
177fd3a15b8821fd949014ac7087ae73f5a11cf96c305e4767f6e1681639f513 | Python | 66,452 | 1,446 | import warnings
from typing import Sequence
import numpy as np
import torch
from torch import nn
from torch.nn import Parameter
from torch.nn import functional as F
from .base import ConfigurationError, Readout
class Gaussian2d(Readout):
"""
Instantiates an object that can used to learn a point in the core ... |
da4cde58dd539d3d846130b04a045327492e105fa8d8d4e2101ca840d1e64221 | Python | 66,558 | 2,267 | """=====================
Read mapping pipeline
=====================
The read mapping pipeline imports unmapped reads from one or more
NGS experiments and maps reads against a reference genome.
This pipeline works on a single genome.
Overview
========
The pipeline implements various mappers. It can be used for
* ... |
505c62a684359b1f2a36f03e3c67c0a7161faf643993f45955c7c089ecab34fd | Python | 66,687 | 1,406 | """
Svetlana dock widget module
"""
import functools
import os
import pickle
import random
from typing import Any
import cv2
import dask.dataframe
import matplotlib.pyplot as plt
from napari_plugin_engine import napari_hook_implementation
from napari.utils.notifications import show_info, notification_manager
import t... |
7bad7fb40f33208882945a703d5d3349ead443ee29343a6f75a58951120ab3fc | Python | 66,907 | 1,571 | import pycircstat
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import efel
from scipy.signal import hilbert
from matplotlib.backends.backend_pdf import PdfPages
import seaborn as sn
from scipy.stats import pearsonr
from copy import copy
from matplotlib.patches import Rectangle
#PV... |
4185c5de5cc4abf8c4bb43ef4d19dbbc0e59f9871cadf033ca04c8836d7ac44f | Python | 66,908 | 1,316 | #!/usr/bin/python3
# Allow direct execution from the repository root, e.g.
# ``python bernn/dl/train/train_ae_classifier_holdout.py``.
import sys
from pathlib import Path
_repo_root = Path(__file__).resolve().parents[3]
if str(_repo_root) not in sys.path:
sys.path.insert(0, str(_repo_root))
import os
import matpl... |
b83e2d1f53450f6f825b972fda24b4d5d2014a5d32b805a6842a255d82b9a769 | Python | 67,138 | 1,801 | from abc import ABC, abstractmethod
from typing import Optional, Sequence, Tuple, Union
import numpy as np
import torch
import torch.nn.functional as F
from bindsnet.utils import im2col_indices
from torch.nn import Module, Parameter
from torch.nn.modules.utils import _pair, _triple
from bindsnet.network.nodes import ... |
f031fae592aec4e17e56daf0e92cbbede9010461bc7460dcbf4e776f73e01798 | Python | 67,167 | 1,938 | """Test base chat model."""
import uuid
import warnings
from collections.abc import AsyncIterator, Iterator
from contextlib import contextmanager
from importlib.metadata import PackageNotFoundError
from typing import TYPE_CHECKING, Any, Literal, get_type_hints
from unittest.mock import patch
import pytest
from langsm... |
9fcbe6010ac709a173fd2d612ca3617be6b7676395f74a477f200e3415575fcf | Python | 67,339 | 1,871 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
import json
from pathlib import Path
from statistics import mean
import dash
import dash_bio.utils.ngl_parser as ngl_parser
import dash_bootstrap_components as dbc
import numpy
import numpy as np
import plotly.graph_objects as go
from dash import Input, Output, State, ht... |
0e7e7cce96a6fe3e4f12b14adcd7ba90c0520c51c7392bf29c7440893866de6b | Python | 67,464 | 1,421 | """Main training entry point for pre-training and downstream fine-tuning.
"""
import json
import os
import random
import time
import math
from functools import wraps
from typing import Callable, List, Sequence
import fsspec
import hydra
import pytorch_lightning as pl
import torch
import torch.nn.functional as F
impo... |
411545fd4a2f8fd1db29899c4f404fb05eb1b2d74ade20c029492e990eb3bec5 | Python | 67,556 | 1,698 | ####################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for detai... |
2ceff28fbb3a57f14ac22aac8eb5c0b4a07f9f09ec12ad470a9356c7d126407f | Python | 67,564 | 1,407 | import json
import logging
import os
import platform
import random
import shutil
import time
import traceback
import warnings
from distutils.version import LooseVersion
from pathlib import Path
from typing import Literal, Sequence, Tuple, Union
import dask.array as da
import numpy as np
import scipy
import scipy.ndima... |
aa4c6d59adea1e7a0234e977c4ea2be3d03e862b46e5a18416f4ea36ce59373a | Python | 67,572 | 1,698 | ####################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for d... |
85fe2accb1d18b13981cda9ec0fb56375d6d58ec6669d03cf7682e74bfe4b091 | Python | 68,178 | 1,215 | ###########################################
# IMPORTS
###########################################
from simtk.openmm import app
from simtk import unit, openmm
import numpy as np
import os
import random
from nose.tools import nottest
from pkg_resources import resource_filename
from perses.annihilation.relative import H... |
3afc6b22ebbbb1b8b081c0f3b7aded68ebdf94fb58752f4614fdd61d81896f57 | Python | 68,378 | 1,844 | import glob
import inspect
import logging
import pickle
import platform
import random
import shutil
import tempfile
import time
import types
from functools import lru_cache
from pathlib import Path
from typing import List, Literal, Tuple, Union
import awkward as ak
import dask.array as da
import h5py
import numpy as n... |
40512bca609e99d8d6978b3a700869c4457ba24b65c1b7b36f920294b6ab7caf | Python | 68,475 | 1,819 |
# Version: 0.18
"""The Versioneer - like a rocketeer, but for versions.
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, 3.5, 3.6, and pypy
* [![Latest Version]
... |
56a1a49cd22fbcec1a59bd5bd2866823714a2e02dcd31b32d361588d1374a788 | Python | 68,801 | 1,790 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of... |
7f3ef7f73f5b822148ed14ba861079c0cffb24986449afc8dff12c4e515d5d67 | Python | 69,327 | 2,164 | """Module that contains tests for runnable.astream_events API."""
import asyncio
import sys
from collections.abc import AsyncIterator, Mapping, Sequence
from itertools import cycle
from typing import Any, cast
import pytest
from pydantic import BaseModel
from typing_extensions import override
from langchain_core.cal... |
18f0dcdf2884b58fa832e5570473bd159fd8cede6ac76b60d939413354cb53d6 | Python | 69,724 | 1,189 | import numpy as np
import pandas as pd
from bernn.utils.utils import get_unique_labels
from sklearn.model_selection import StratifiedGroupKFold, StratifiedKFold
from bernn.dl.models.pytorch.utils.dataset import MSCSV, MS2CSV
def get_alzheimer(path, args, seed=42):
"""
Args:
path: Path where data is loc... |
75899351026d0035fb8e8a0ad13559224caefc855145342ae3e7db4d47d375ce | Python | 70,144 | 1,855 |
# Version: 0.19
"""The Versioneer - like a rocketeer, but for versions.
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/python-versioneer/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible with: Python 3.6, 3.7, 3.8, 3.9 and pypy3
* [![Latest Version][pyp... |
8918b8a6d09c117932fac8f3188dbdf06892f95c7e45badaf45fc63337af7792 | Python | 70,989 | 1,649 | import numpy as np
import torch
from scipy import stats
import matplotlib.pyplot as plt
import os
import pickle
from networks import SstVipNetworkFull
from exc_vip_sst_net import SstVipExcNetwork
from exc_vip_sst_net import SstVipExcNetworkComplete
from exc_vip_sst_net import SstVipExcPvNetwork
from stim_change_task... |
6b45bbb1d6e4e5c8322a4740fc2743cda4c490cbd813c1e4ccbc0551598506e4 | Python | 71,132 | 1,256 | ###########################################
# IMPORTS
###########################################
from simtk.openmm import app
from simtk import unit, openmm
import numpy as np
import os
import random
from nose.tools import nottest
from pkg_resources import resource_filename
from perses.annihilation.relative import H... |
c42d56eebd66f3bda6abf3e9ae29ebc5ffaa1527518804dae6def376aa225825 | Python | 71,143 | 1,629 | """Wrapper classes for Cif input and output from Structures."""
from __future__ import annotations
import math
import os
import re
import textwrap
import warnings
from collections import defaultdict, deque
from datetime import datetime
from functools import partial
from inspect import getfullargspec as getargspec
fro... |
8a791872f4ea07f64cb79a2331eed97969f3df93a8e8dae1eaa483b4ed5acd09 | Python | 71,579 | 1,693 | ####################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for detai... |
4ebcc461bc0013bb2a4f22f0dbaaf90a9d5b2551304868258788861350135f99 | Python | 71,604 | 1,487 | """
Tools for computing atom mappings for relative free energy transformations.
These tools currently require the OpenEye Toolkit, but will eventually be fully migrated
to the OpenFF toolkit.
.. todo :: This module should be migrated to openmmtools.
"""
from simtk import unit
import copy
import os
import numpy as ... |
a2f7b4f18aaa3f6db1399f224f6303691cb46ac3b9ba36bf1aa87704a504edd1 | Python | 71,669 | 1,948 | """Base classes and utilities for LangChain tools."""
from __future__ import annotations
import functools
import inspect
import json
import logging
import typing
import warnings
from abc import ABC, abstractmethod
from collections.abc import Callable, Mapping, Sequence
from typing import (
TYPE_CHECKING,
Anno... |
14ae8727a15a96fd629e1cb589cea221c17ea3d3f0dadaecf18450a1b3e58858 | Python | 71,903 | 1,850 | from collections import deque
from collections.abc import Hashable, Iterable
from itertools import combinations
from typing import Any
import networkx as nx
import pandas as pd
from pgmpy.base._algorithms import _GraphAlgorithms
from pgmpy.base._mixin_roles import _GraphRolesMixin
from pgmpy.base._plotting import _Gr... |
52c05d1c846d6e34a5f44f5c831892b0e2db05fa49fd1f33b48811de146a5b6c | Python | 72,071 | 1,264 | import numpy as np
import matplotlib.pyplot as plt
import matplotlib.gridspec as gridspec
from matplotlib.lines import Line2D
from matplotlib.patches import Patch
from Articles.Sequential_Learning_Striatum.Figures.cfg_color import colors
from Articles.Sequential_Learning_Striatum.Figures.FigureSequential \
import... |
aeded5b19a93dfc568fa609cd225fa3e4e02ea308001a9b7fe5314131f2540a8 | Python | 72,204 | 1,457 | """
Unit tests for NCMC switching engine.
"""
__author__ = 'John D. Chodera'
################################################################################
# IMPORTS
################################################################################
import copy
from simtk import openmm, unit
from simtk.openmm import ... |
038bc9429296a777865ba91608abccb548c6b1a5b5e5643ddea2df440f08e7d0 | Python | 72,270 | 2,014 | #!/usr/bin/python
#############################################################################
#Package: stamp
#Updated by Yiqin Wang
#Usage:
#
#
##############################################################################
#the path to the executables
samtools = "samtools-1.6"
bwa ="bwa-0.7.17"
bamleftalign="bamle... |
d9d9452efc1bd954d2cf145e443c2224e6b4e1e11d1758ae0608df87d83ca225 | Python | 72,673 | 1,475 | # os.environ['CUDA_VISIBLE_DEVICES'] = '-1'
# CUDA_VISIBLE_DEVICES = ""
import os
from tensorboard.plugins.hparams import api as hp
import tensorflow as tf
from sklearn.metrics import silhouette_score, adjusted_rand_score, adjusted_mutual_info_score
from bernn.dl.models.pytorch.utils.metrics import rKBET, rLISI
import... |
aa6292ead6e5deceaba2bdbe830d362ef071dda12365894d73e9f330d29b68b9 | Python | 73,020 | 1,815 | """
A modified version of the original Scholar implementation by Dallas Card to
support survival analysis supervision (Cox and several parametric AFT losses)
and where we encourage sparsity via l1 regularization; note that currently the
only topic model supported here is SAGE
The original Scholar code that this file i... |
91a86b63e2daec99498c5ec2b5be98ee1cd31df90d3abfe2ac36a6339d0aa981 | Python | 73,286 | 1,668 | """Wrapper classes for Cif input and output from Structures."""
from __future__ import annotations
import math
import os
import re
import textwrap
import warnings
from collections import defaultdict, deque
from datetime import datetime
from functools import partial
from inspect import getfullargspec as getargspec
fro... |
6ff4975a882a5ae456f5843682b38dd846301f69a601775966c2d03fff429823 | Python | 73,646 | 1,942 | # Copyright Generate Biomedicines, Inc.
#
# 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 ... |
bf3d2eb1b27a71050e03433f53903d6ae326d836b29c1ced9aaeea0e07b65dc9 | Python | 73,695 | 1,814 | # Copyright 2024 DeepMind Technologies Limited
#
# AlphaFold 3 source code is 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... |
30dc271dcd02f7cef012f0935651a941c76eb6a4736824047aaa3dd7c2dcf854 | Python | 73,932 | 2,006 | import re
import warnings
from pathlib import Path
from typing import Any
import pytest
from packaging import version
from pydantic import ValidationError
from syrupy.assertion import SnapshotAssertion
from langchain_core.load import dumpd, load
from langchain_core.messages import (
AIMessage,
BaseMessage,
... |
b73f40d2131a7d72b1ed2b1926b0de0ea130fddefbe78af5f6c9853eb3216afb | Python | 74,492 | 1,878 | import warnings
from collections import OrderedDict
import numpy as np
import torch
from torch import nn as nn
from torch.nn import ModuleDict, Parameter
from torch.nn import functional as F
from ..constraints import positive
class ConfigurationError(Exception):
pass
# ------------------ Base Classes --------... |
2ff3a2c9a4769984c3dd2072f922f75e9edfacb0737e374e2554ee72ae9ae0e6 | Python | 74,538 | 1,656 | import inspect
import logging
import pickle
import tempfile
import traceback
from collections import defaultdict
from pathlib import Path
from typing import Literal, Tuple, Union
import fastcluster
import hdbscan
import networkx as nx
import numpy as np
import pandas as pd
import seaborn as sns
from dask import array ... |
b75d37a69a1e05b0edb67c17e3e200da0ba8eec963be4c257ba063c8dd5e342c | Python | 74,827 | 1,583 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri May 28 2021
@author: Simon Pelletier
"""
import os
import csv
from PIL import Image
import torch
import itertools
import numpy as np
from torch.utils.data import Dataset
import random
import pandas as pd
from sklearn.preprocessing import minmax_scale as... |
8d7dec4d681ea4a92583a72ceeeab4be9eab465dab94af23abb1e998eaef639d | Python | 75,123 | 2,376 | # -*- coding: utf-8 -*-
"""
Created on Thu Aug 6 00:21:15 2020
@author: Xingyan Liu
Functions for handling AnnData:
* I/O functions
* preprocessing
- normalization / z-scoring / ...
- groups / ...
* statistics computation
"""
import logging
import os
from pathlib import Path
from typin... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.