ObjectiveThe primary objective of this study was to analyze CpG dinucleotide dynamics in coronaviruses by comparing Wuhan-Hu-1 with its closest and most distant relatives. Heatmaps were generated to visualize CpG counts and O/E ratios across intergenic regions, providing a clear depiction of conserved and divergent CpG patterns.Methods1. Data CollectionSource : The dataset includes CpG counts and O/E ratios for various coronaviruses, extracted from publicly available genomic sequences.Format : Data was compiled into a CSV file containing columns for intergenic regions, CpG counts, and O/E ratios for each virus.2. PreprocessingData Cleaning :Missing values (NaN), infinite values (inf, -inf), and blank entries were handled using Python's pandas library.Missing values were replaced with column means, and infinite values were capped at a large finite value (1e9).Reshaping :The data was reshaped into matrices for CpG counts and O/E ratios using meltpandas[] and pivot[] functions.3. Distance CalculationEuclidean Distance :Pairwise Euclidean distances were calculated between Wuhan-Hu-1 and other viruses using the scipy.spatial.distance.euclidean function.Distances were computed separately for CpG counts and O/E ratios, and the total distance was derived as the sum of both metrics.4. Identification of Closest and Distant RelativesThe virus with the smallest total distance was identified as the closest relative .The virus with the largest total distance was identified as the most distant relative .5. Heatmap GenerationTools :Heatmaps were generated using Python's seaborn library (sns.heatmap) and matplotlib for visualization.Parameters :Heatmaps were annotated with numerical values for clarity.A color gradient (coolwarm) was used to represent varying CpG counts and O/E ratios.Titles and axis labels were added to describe the comparison between Wuhan-Hu-1 and its relatives.ResultsClosest Relative :The closest relative to Wuhan-Hu-1 was identified based on the smallest Euclidean distance.Heatmaps for CpG counts and O/E ratios show high similarity in specific intergenic regions.Most Distant Relative :The most distant relative was identified based on the largest Euclidean distance.Heatmaps reveal significant differences in CpG dynamics compared to Wuhan-Hu-1 .Tools and LibrariesThe following tools and libraries were used in this analysis:Programming Language :Python 3.13Libraries :pandas: For data manipulation and cleaning.numpy: For numerical operations and handling missing/infinite values.scipy.spatial.distance: For calculating Euclidean distances.seaborn: For generating heatmaps.matplotlib: For additional visualization enhancements.File Formats :Input: CSV files containing CpG counts and O/E ratios.Output: PNG images of heatmaps.Files IncludedCSV File :Contains the raw data of CpG counts and O/E ratios for all viruses.Heatmap Images :Heatmaps for CpG counts and O/E ratios comparing Wuhan-Hu-1 with its closest and most distant relatives.Python Script :Full Python code used for data processing, distance calculation, and heatmap generation.Usage NotesResearchers can use this dataset to further explore the evolutionary dynamics of CpG dinucleotides in coronaviruses.The Python script can be adapted to analyze other viral genomes or datasets.Heatmaps provide a visual summary of CpG dynamics, aiding in hypothesis generation and experimental design.AcknowledgmentsSpecial thanks to the open-source community for developing tools like pandas, numpy, seaborn, and matplotlib.This work was conducted as part of an independent research project in molecular biology and bioinformatics.LicenseThis dataset is shared under the CC BY 4.0 License , allowing others to share and adapt the material as long as proper attribution is given.DOI: 10.6084/m9.figshare.28736501

{"Description This code analyzes the impact of chanting the Hare Krishna mantra on the body's chakras using Python. It visualizes the cumulative energy distribution across the chakras during the chant and provides statistical analysis of the energy levels. Imports: numpy: For numerical operations and array handling. matplotlib.pyplot: For plotting the heatmap and bar charts. seaborn: For creating aesthetically pleasing statistical graphics. Define the Mantra and Chakra Associations: mantra_sequence: A list representing the sequence of words in the Hare Krishna mantra. chakra_association: A dictionary mapping each word in the mantra to its associated chakras, represented as binary lists (1 for activation, 0 for no activation). Initialize Chakra Energy Levels: chakra_levels: A 2D array initialized with zeros to store the energy levels for each chakra throughout the mantra sequence. Calculate Cumulative Impact on Chakras: Iterate through each word in the mantra sequence. For each word, update the corresponding chakra energy levels by accumulating the impact values. Generate Heatmap for Chakra Energy Distribution: Create a heatmap to visualize the energy distribution across the chakras for each word in the mantra sequence. Customize the heatmap with labels for the chakras and chant sequence. Statistical Analysis: Compute the mean and standard deviation of the energy levels for each chakra. Plot these statistical measures using a bar chart to compare the average energy levels and their variability across different chakras."}

import pandas as pd import numpy as np

PERFORMING EDA

data.head() data.info()

attributes_data = data.iloc[:, 1:] attributes_data

attributes_data.describe() attributes_data.corr()

import seaborn as sns import matplotlib.pyplot as plt

Calculate correlation matrix

correlation_matrix = attributes_data.corr() plt.figure(figsize=(18, 10))

Create a heatmap

sns.heatmap(correlation_matrix, annot=True, cmap='coolwarm') plt.show()

CHECKING IF DATASET IS LINEAR OR NON-LINEAR

Calculate correlations between target and predictor columns

correlations = data.corr()['Diabetes_binary'].drop('Diabetes_binary')

Create a bar chart

plt.figure(figsize=(10, 6)) correlations.plot(kind='bar') plt.xlabel('Predictor Columns') plt.ylabel('Correlation values') plt.title('Correlation between Diabetes_binary and Predictors') plt.show()

CHECKING FOR NULL AND MISSING VALUES, CLEANING THEM

Count the number of null values in each column

print(data.isnull().sum())

to check for missing values in all columns

print(data.isna().sum())

LASSO import numpy as np import pandas as pd import matplotlib.pyplot as plt from sklearn.linear_model import Lasso from sklearn.model_selection import train_test_split from sklearn.model_selection import GridSearchCV, KFold

X = data.iloc[:, 1:] y = data.iloc[:, 0] X_train, X_test, y_train, y_test = train_test_split(X, y, test_size = 0.3, random_state = 42)

gridsearchcv is used to find the optimal combination of hyperparameters for a given model

So, in the end, we can select the best parameters from the listed hyperparameters.

parameters = {"alpha": np.arange(0.00001, 10, 500)}
kfold = KFold(n_splits = 10, shuffle=True, random_state = 42) lassoReg = Lasso() lasso_cv = GridSearchCV(lassoReg, param_grid = parameters, cv = kfold) lasso_cv.fit(X, y) print("Best Params {}".format(lasso_cv.best_params_))

column_names = list(data) column_names = column_names[1:] column_names

lassoModel = Lasso(alpha = 0.00001) lassoModel.fit(X_train, y_train) lasso_coeff = np.abs(lassoModel.coef_)#making all coefficients positive plt.bar(column_names, lasso_coeff, color = 'orange') plt.xticks(rotation=90) plt.grid() plt.title("Feature Selection Based on Lasso") plt.xlabel("Features") plt.ylabel("Importance") plt.ylim(0, 0.16) plt.show()

RFE from sklearn.model_selection import train_test_split X_train, X_test, y_train, y_test = train_test_split(X, y, test_size = 0.3, random_state = 42)

from sklearn.feature_selection import RFECV from sklearn.tree import DecisionTreeClassifier model = DecisionTreeClassifier() rfecv = RFECV(estimator= model, step = 1, cv = 20, scoring="accuracy") rfecv = rfecv.fit(X_train, y_train)

num_features_selected = len(rfecv.rankin_)

Cross-validation scores

cv_scores = rfecv.ranking_

Plotting the number of features vs. cross-validation score

plt.figure(figsize=(10, 6)) plt.xlabel("Number of features selected") plt.ylabel("Score (accuracy)") plt.plot(range(1, num_features_selected + 1), cv_scores, marker='o', color='r') plt.xticks(range(1, num_features_selected + 1)) # Set x-ticks to integers plt.grid() plt.title("RFECV: Number of Features vs. Score(accuracy)") plt.show()

print("The optimal number of features:", rfecv.n_features_) print("Best features:", X_train.columns[rfecv.support_])

PCA import pandas as pd import numpy as np import matplotlib.pyplot as plt %matplotlib inline from sklearn.decomposition import PCA from sklearn.preprocessing import StandardScaler

X = data.drop(["Diabetes_binary"], axis=1) y = data["Diabetes_binary"]

df1=pd.DataFrame(data = data,columns=data.columns) print(df1)

scaling=StandardScaler() scaling.fit(df1) Scaled_data=scaling.transform(df1) principal=PCA(n_components=3) principal.fit(Scaled_data) x=principal.transform(Scaled_data) print(x.shape)

principal.components_

plt.figure(figsize=(10,10))

plt.scatter(x[:,0],x[:,1],c=data['Diabetes_binary'],cmap='plasma') plt.xlabel('pc1') plt.ylabel('pc2')

print(principal.explained_variance_ratio_)

T-SNE from sklearn.manifold import TSNE from numpy import reshape import seaborn as sns

tsne = TSNE(n_components=3, verbose=1, random_state=42) z = tsne.fit_transform(X)

df = pd.DataFrame() df["y"] = y df["comp-1"] = z[:,0] df["comp-2"] = z[:,1] df["comp-3"] = z[:,2] sns.scatterplot(x="comp-1", y="comp-2", hue=df.y.tolist(), palette=sns.color_palette("husl", 2), data=df).set(title="Diabetes data T-SNE projection")

Suicidal Behaviors and Attempts

Lethality, Risk Factors, and Statuses

By [source]

About this dataset

More Datasets

For more datasets, click here.

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• 🚨 Your notebook can be here! 🚨!

How to use the dataset

Before you begin your analysis, it is important that you are familiar with the dataset: - The columns include: User (a unique identifier for each user), Post (provides text of each post), Label (indicates whether a post is associated with suicidal behavior or not).
- Each row in this dataset provides detailed information regarding one user’s post on Reddit related to suicide.

Now that you have an understanding of what’s included in this set, let's dive into working with it! First off, we recommend exploring within Jupyter Notebook given its ease of use and interactive nature - just open up a new notebook in Kaggle Notebooks. Here are some helpful tips:

• Explore Data Types : Take some time getting familiarized with what type of data is found in each column by using various commands such as .dtypes or .info(). Knowing which type each column holds will make it easier when filtering columns later on. You could also explore any missing values using .isnull().sum() command which provides a good indication if any preprocessing such as filling missing values needs to take place prior to analysis.

• Analyze Labels & Posts : Have a better understanding of labels attached to posts using value_counts() command which helps summarize proportions between these two variables so that more informed decisions can be made later on during analysis/modeling stages. Having an understanding when dealing real world problems often requires analyzing different aspects/labels associated before proceeding further so take your time here! For example, grouping posts based on labels can be done via groupby(Label).

• Visualize your Results : Visualization makes findings easier to interpret; try leveraging matplotlib packages such as plt xy or seaborn sns heatmap; alternatively use Tableau externally once data preparation has been completed previously within Jupyter Notebook along side Python libraries like Scikit Learn or Numpy used for modeling techniques such machine learning algorithm implementations or complex computations like linear algebraic analyses respectively should there ever come an instance were

Research Ideas

• Analyzing which risk factors associated with suicidal behavior are most prevalent in certain demographic groups, such as gender and age.
• Examining the potential outcomes of different methods of self-harm and understanding their lethality levels to create more effective prevention and response strategies.
• Creating predictive models for mental health workers to use when assessing individuals at risk of suicide so they can identify individuals who may need immediate intervention or follow up care

Acknowledgements

If you use this dataset in your research, please credit the original authors. Data Source

License

License: CC0 1.0 Universal (CC0 1.0) - Public Domain Dedication No Copyright - You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. See Other Information.

Columns

File: 500_Reddit_users_posts_labels.csv | Column name | Description | |:--------------|:------------------------------------------------------------------------------------| | User | Unique identifier for each user. (String) | | Post | Text of the post. (String) | | Label | Label indicating whether the post is related to suicidal behavior or not. (Boolean) |

Acknowledgements

If you use this dataset in your research, please credit the original authors. If you use this dataset in your research, please credit .