Datasets:
OpenScientificCodeRegistry
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# %% [markdown] # # ReedBMI # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weights-in...
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# %% [markdown] # # SenCultureAge # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weig...
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# %% [markdown] # # Training Regression Models on chemical reactions # # > Here we show how simple it is to train reaction BERTs on any regression task. # %% [markdown] # ## Available tools # # BERT and related transformer models have revolutionised Natural Language Processing. The implementation of such models is c...
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# %% [markdown] # # epiTOC1 # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weights-in...
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# %% [markdown] # # CVDWesterman # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weigh...
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# %% [markdown] # # CellPopAge # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weights...
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# %% [markdown] # # Meer # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weights-into-...
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# %% [markdown] # # Petkovich # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weights-...
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# %% [markdown] # # CorticalClock # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weig...
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# %% [markdown] # # LeeRobust # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weights-...
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# %% [markdown] # # LeeControl # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weights...
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# %% [markdown] # # ZhangMortality # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-wei...
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# %% import matplotlib.pyplot as plt from matplotlib_venn import venn2 from matplotlib_venn import venn3 import xlrd import xlsxwriter import matplotlib matplotlib.rcParams['pdf.fonttype'] = 42 matplotlib.rcParams['ps.fonttype'] = 42 namea='FS1094_proteinGroups (1)' nameb='pMG_20210621_microglia proteomics raw data' na...
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# %% [markdown] # # Bohlin # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weights-int...
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# %% [markdown] # # EnsembleAgeStatic # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-...
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# %% # -*- coding: utf-8 -*- """ Created on Wed Sep 14 14:13:34 2022 @author: dmc lab ION Grad Bootcamp 2022 Widefield Data Analysis """ import os import numpy as np import easygui import tifffile import glob from skimage import io from skimage.measure import block_reduce import matplotlib.pyplot as plt from matplot...
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# %% [markdown] # # stemTOC # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weights-in...
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# %% [markdown] # # Weidner # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weights-in...
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# %% [markdown] # # DunedinPoAm38 # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weig...
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# %% [markdown] # # Pasta # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weights-into...
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# %% [markdown] # # Setup # ## Goals # # 1. Identify cell types captured in MS1 that express analytes assayed in both in-house and Evetech cytokine assays # # ## Import packages # %% import scanpy as sc import pandas as pd import numpy as np import os # %% print(sc.__version__) print(pd.__version_...
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# %% [markdown] # # DNAmIC # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weights-int...
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# %% [markdown] # # MammalianFemale # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-we...
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# %% [markdown] # # LeeRefinedRobust # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-w...
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# %% [markdown] # # EnsembleAgeStaticTop # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Lo...
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# %% [markdown] # # SCH23390 TFC Analysis # # ### Table of Contents # # 1. [Experiment Info](#ei) # 2. [Imports and Set Up](#is) # 3. [Training](#tr) # 1. [Load and Clean Training Data](#lctr) # 2. [Plot Training Data](#pltr) # 4. [Tone Test](#to) # 1. [Load and Clean Tone Test Data](#lcto) # 2. [Plot...
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# %% [markdown] # # GliaSin # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weights-in...
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# %% [markdown] # # YingCausAge # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weight...
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# %% [markdown] # # Knight # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weights-int...
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# %% [markdown] # # Notebook for training Dev-ResNet with Triplet Semi-Hard loss # # A notebook outlining the training and inference process for Dev-ResNet with Triplet Semi-Hard loss, for the purpose of visualising the differences between detected features in high-dimensional space between developmental events. Note ...
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# %% import os os.environ['QT_QPA_PLATFORM']='offscreen' import ete3 from ete3 import Tree, TreeStyle, NodeStyle, faces, SeqMotifFace, TextFace, CircleFace import pandas as pd import urllib.request from pathlib import Path import numpy as np import matplotlib # %% output_dir = "figs" # %% for f,url in (("../data/exp...
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# %% [markdown] # # sPYcon Tutorial # %% [markdown] # sPYcon is a toolbox to easily use and benchmark connectivity inference algorthims. In the following basic functionalities are explained step by step. # %% # Basic imports from matplotlib import pyplot import numpy # %% #spycon_test = load_test(name='ren_simulatio...
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# %% [markdown] # # HepatoXu # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weights-i...
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# %% [markdown] # # RepliTali # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weights-...
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# %% [markdown] # # McCartneyWHR # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weigh...
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# %% [markdown] # # EnsembleAgeHumanMouse # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#L...
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# %% [markdown] # # CompIL6 # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weights-in...
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# %% [markdown] # # Clustering compounds based on the similarity of their Morgan fingerprints # %% [markdown] # You are going to use a Jupyter notebook originally featured in our Nature Protocols paper. # # Please cite: Tran-Nguyen, V. K., Junaid, M., Simeon, S. & Ballester, P. J. A practical guide to machine-learnin...
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# %% [markdown] # # DepressionBarbu # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-we...
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# %% [markdown] # # YingDamAge # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weights...
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# %% [markdown] # # SkinAndBlood # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weigh...
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# %% [markdown] # # YingAdaptAge # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weigh...
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# %% [markdown] # # LC ChR2 65dB 0.2mA TFC 180s ITI Analysis # # ### Table of Contents # # 1. [Experiment Info](#ei) # 2. [Imports and Set Up](#is) # 3. [Training](#tr) # 1. [Load and Clean Training Data](#lctr) # 2. [Plot Training Data](#pltr) # 4. [Tone Test](#to) # 1. [Load and Clean Tone Test Data](#l...
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# %% #Basics import matplotlib.pyplot as plt import matplotlib import numpy as np import sys import os import csv import time import random import pandas as pd # %% val_file = pd.read_csv('/home/kvattis/Documents/data/train_dataset_control_AT_Mel_Spec_2022_noise_red2_severity_v9.csv', names=["P_ID", "Address", "Label"...
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# %% [markdown] # # McCartneyTotalHDLRatio # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#...
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# %% import matplotlib %matplotlib inline import numpy as np import matplotlib.pyplot as plt from helper import * from tqdm import tqdm_notebook import brainconn as bc import pandas as pd import seaborn as sns import nilearn.plotting as plotting import palettable as pal import matplotlib.colors as mcolors import matpl...
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# %% [markdown] # # ZhangBLUP # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weights-...
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# %% [markdown] # # HypoClock # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weights-...
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# %% [markdown] # # SmokingMcCartney # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-w...
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# %% import pandas as pd import seaborn as sns import numpy as np import matplotlib.pyplot as plt #from sklearn.metrics import roc_curve, auc, RocCurveDisplay, precision_recall_curve, PrecisionRecallDisplay #from helpers import read_metrics_csvs, read_fastas import math from sklearn.metrics import roc_curve, auc, RocCu...
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# %% [markdown] # # Computing the Morgan fingerprints of molecules and comparing them # %% [markdown] # You are going to use a Jupyter notebook originally featured in our Nature Protocols paper. # # Please cite: Tran-Nguyen, V. K., Junaid, M., Simeon, S. & Ballester, P. J. A practical guide to machine-learning scori...
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# %% [markdown] # # ZhangEN # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weights-in...
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# %% [markdown] # # LC GcAMP Tone Only Analysis # %% import matplotlib.pyplot as plt %matplotlib inline import pandas as pd import numpy as np import sys # change pkg_path variable to the directory storing the package sys.path.insert(0, '../utility_code') import fp_dat, fp_viz import seaborn as sns import statsmodels....
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# %% [markdown] # # GrimAge2ADM # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weight...
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# %% [markdown] # # McCartneyAlcohol # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-w...
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# %% [markdown] # # GrimAge2Leptin # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-wei...
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# %% [markdown] # # Thompson # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weights-i...
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# %% [markdown] # [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/lucascamillomd/pyaging/blob/main/tutorials/tutorial_blood_chemistry.ipynb) [![Open In nbviewer](https://img.shields.io/badge/View%20in-nbviewer-orange)](https://nbviewer.jupyter.org/gi...
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# %% [markdown] # # GrimAge2LogA1C # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-wei...
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# %% [markdown] # # DeconvoluteBloodEPIC # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Lo...
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# %% [markdown] # # DNAmStress # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weights...
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# %% [markdown] # # DeconvoluteBloodEPIC # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Lo...
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# %% [markdown] # # GrimAge2CystatinC # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-...
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# %% [markdown] # # GrimAge2LogCRP # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-wei...
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# %% [markdown] # # GrimAge2PackYrs # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-we...
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# %% [markdown] # # DeconvoluteBloodEPIC # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Lo...
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# %% [markdown] # # DeconvoluteBloodEPIC # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Lo...
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# %% [markdown] # # DeconvoluteBloodEPIC # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Lo...
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# %% from pathlib import Path import sys from dotenv import load_dotenv, find_dotenv load_dotenv() PROJECT_ROOT = Path(find_dotenv()).parent sys.path.append(str(PROJECT_ROOT.joinpath('src'))) print(f"Project root directory: {PROJECT_ROOT}") # %% import numpy as np import plotly.graph_objects as go # %% # function to...
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# %% [markdown] # # GrimAge2PAI1 # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weigh...
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# %% [markdown] # # Template # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weights-i...
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# %% [markdown] # # DeconvoluteBloodEPIC # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Lo...
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# %% [markdown] # # Training notebook for training and evaluating the an equivalent 2D version of Dev-ResNet: ResNet18 # # A notebook outlining the training and evaluation procedure for ResNet18, an equivalent residual CNN to Dev-ResNet. Note that this is specifically set up in terms of parameters for a dataset compr...
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# %% [markdown] # # GrimAge2GDF15 # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weig...
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# %% [markdown] # # GrimAge2B2M # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weight...
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# %% [markdown] # # DunedinPACE # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weight...
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# %% %matplotlib inline import os, glob import numpy as np import matplotlib.pyplot as plt import matplotlib as mpl from scipy.optimize import curve_fit import scipy.optimize as opt import matplotlib.lines as mlines import pandas as pd import csv from skimage import io from matplotlib.gridspec import GridSpec from scip...
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# %% [markdown] # # GrimAge2TIMP1 # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weig...
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# %% [markdown] # # McCartneyBodyFat # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-w...
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# %% [markdown] # # Plotting chromosight's output # # Chromosight generates tabular text files with loops coordinates and scores. This file can be loaded into your favorite scripting language for visualization. For the purpose of this demonstration, we show how to plot the contact maps with detected coordinates using ...
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# %% [markdown] # # ProstateCancerKirby # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Loa...
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# %% [markdown] # # Read in data # %% if (!require("tidyverse")) install.packages("tidyverse") #if (!require("VIM")) install.packages("VIM") #if (!require("Amelia")) install.packages("Amelia") #if (!require("naniar")) install.packages("naniar") #if (!require("visdat")) install.packages("visdat") #if (!require("SparseM...
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# %% [markdown] # # OcampoATAC1 # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weight...
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# %% [markdown] # # McCartneyBMI # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weigh...
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# %% [markdown] # # McCartneyHDLCholesterol # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](...
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# %% [markdown] # # McCartneyEducation # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load...
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# %% import warnings warnings.filterwarnings("ignore") from fmriprep_denoise.dataset.atlas import ATLAS_METADATA from fmriprep_denoise.visualization import figures, utils import ipywidgets as widgets from ipywidgets import interactive, interact path_root = utils.repo2data_path() / "denoise-metrics" # %% [markdown]...
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# %% import scanpy as sc import pandas as pd import numpy as np import sklearn.metrics import torch import torch.nn as nn from torch.optim import Adam import torch.utils.data as Data from sklearn.model_selection import train_test_split from sklearn.metrics import f1_score from collections import Counter # %% label = s...
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# %% [markdown] # # McCartneyTotalCholesterol # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model...
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# %% [markdown] # # PhenoAge # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weights-i...
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# %% [markdown] # # Command line interface # # The PCNtoolkit is a python package, but it can also be used from the command line. # # Here we show how to use the PCNtoolkit from the command line. # # Furthermore, you can use this script to generate commands for the command line interface. (Although if you are able ...
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# %% [markdown] # # McCartneyLDLCholesterol # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](...
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# %% [markdown] # # Training notebook for training and evaluating the Dev-ResNet model # # A notebook outlining the training and evaluation procedure for Dev-ResNet. Note that this is specifically for a dataset comprising developmental sequences of the great pond snail, Lymnaea stagnalis. # # ## Dependencies # # Th...
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# %% [markdown] # # Horvath2013 # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weight...
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# %% [markdown] # # XChrom # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weights-int...
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# %% import scipy as sp import scipy.io import scipy.stats import os import numpy as np import pandas as pd import glob import random as rand from tqdm import tnrange, tqdm_notebook import sys sys.path.append(os.getcwd()+'\\..') import cmocean from utils import utils from utils import zscores## If exporting figures for...
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# %% [markdown] # # YChrom # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weights-int...
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# %% import pandas as pd import numpy as np from pathlib import Path code_dir=Path.cwd() project_dir=code_dir.parent cat_dir=project_dir.parent/"cat12" input_dir=project_dir/"input" output_dir=project_dir/"output/abannotate" tmp_dir=project_dir/"tmp" output_dir.mkdir(exist_ok=True) # %% bootstrap_pls_df_schaefer100 ...
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# %% [markdown] # # RepliTaliNorm # %% [markdown] # ## Index # 1. [Instantiate model class](#Instantiate-model-class) # 2. [Define clock metadata](#Define-clock-metadata) # 3. [Download clock dependencies](#Download-clock-dependencies) # 4. [Load features](#Load-features) # 5. [Load weights into base model](#Load-weig...
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# %% [markdown] # ### ====== Loading, Reconstructing and Visualizing the fastMRI Prostate dataset ====== # # #### To download the fastMRI prostate dataset: https://fastmri.med.nyu.edu/ # %% import argparse import h5py import numpy as np from pathlib import Path from matplotlib import pyplot as plt import xml.etree.E...