# Posts by Category

## Multiple hypothesis testing problem in Bioinformatics

Multiple hypothesis testing and corrections, type I and II errors, false discovery rate, Bonferroni correction, and Benjamini/Hochberg correction

## Statistical hypothesis testing, types of errors, and interpretation of p values

Learn how to propose null and Alternative hypotheses, perform the statistical analysis, and interpret the results

## Find probabilities using discrete and continuous probability distributions

Learn how to use probability distributions, probability mass function (PMF), cumulative distribution function (CDF), and probability density function (PDF)

## Logistic regression in Python (feature selection, model fitting, and prediction)

Logistic regression for prediction of breast cancer, assumptions, feature selection, model fitting, model accuracy, and interpretation

## Multicollinearity and variance inflation factor (VIF) in the regression model (with Python code)

Multicollinearity refers to the significant correlation among the independent variables in the regression model. Variance Inflation Factor (VIF) helps to dia...

## Multiple linear regression (MLR)

Multiple regression analysis using statsmodels. Learn how to define regression model, assumptions, metrics evaluation, and interpretation

## Linear Regression Using Neural Networks (PyTorch)

Linear regression using PyTorch

## Calculating residuals in regression analysis [Manually and with codes]

Learn to calculate residuals in regression analysis manually and with Python and R codes

## Calculate harmonic mean in R (with examples)

Learn what is harmonic mean and how to calculate it in R

## Calculate harmonic mean in Python (with examples)

Learn what is harmonic mean and how to calculate it in Python

## Generate random dataset with normal distribution in Python (using NumPy)

Learn how to generate a random dataset with normal distribution using NumPy

## How to perform Chi-squared (χ2) test for independence in Python (with example)

Learn when to use and how to calculate Chi-squared test for independence

## Perform one sample, two samples, and paired Z-test in R (with example dataset)

Learn when to use Z-test, types of Z-test, assumptions, hypothesis, and formula for each type of test, and Z-test calculation in R

## Perform three types of Z-test in Python (with example dataset)

Learn how to perform one sample, two samples, and paired Z-test in Python. This article also covers when to use Z-test, types of Z-test, assumptions, hypothe...

## Perform three types of t-test in Python

Learn when to use t-test, types of t-test, assumptions, hypothesis, and formula for each type of test, and t-test calculation in Python

## One and Two-sample Z-Test for proportions (with R code)

Learn to perform sample proportions Z-Test in R

## Mann-Whitney U test (Wilcoxon rank sum test) in Python [pandas and SciPy]

Learn when to use Mann-Whitney U test, assumptions, hypothesis, and formula, and test calculation in Python

## Calculator for Mann-Whitney U test (Wilcoxon rank sum test)

Calculate Mann-Whitney U test online calculator

## Durbin-Watson (DW) test for autocorrelation (with R code)

Learn to perform Durbin-Watson test (a test for autocorrelation) in R

## Perform Durbin-Watson (DW) test in Python

Learn to perform Durbin-Watson test (a test for autocorrelation) in Python

## Perform t-test from scratch in Python

Calculate three types of t-test from scratch

## Fisher’s exact test of independence in R [with post-hoc test]

A step-by-step article for performing Fisher’s exact test in R. This article describes the background of Fisher’s exact test, assumptions, hypotheses, codes,...

## Fisher’s exact test of independence in Python [with example]

A step-by-step article for performing Fisher’s exact test in Python

## Fisher’s exact test calculator (with formula)

Online calculator for Fisher’s exact test of independence for 2 x 2 contingency table

## How to calculate correlation between two variables in R

This articles explains Pearson’s, Spearman’s rho, and Kendall’s Tau correlation methods and their calculation in R

## Correlation analysis in Python

Correlation analysis using Python code

## Repeated Measures ANOVA using Python and R (with examples)

Repeated Measure ANOVA in Python and R. This article explains repeated Measure ANOVA model, multiple pairwise comparisons, and results interpretation

## Mixed ANOVA using Python and R (with examples)

Learn to perform mixed ANOVA, check assumptions, and post-hoc tests for significant interactions and main effects

## ANOVA using Python (with examples)

One and two-way ANOVA in Python. This article explains ANOVA model, tables, formula, calculation, multiple pairwise comparisons, and results interpretation

## MANOVA using R (with examples and code)

A step-by-step article for performing MANOVA in R. This article describes the background of MANOVA, assumptions, hypotheses, and codes for performing MANOVA ...

## Friedman test using R (with examples and code)

A step-by-step article for performing Friedman test in R

## Friedman test using Python (with examples and code)

A step-by-step article for performing Friedman test in Python

## ANCOVA using R and Python (with examples and code)

A step-by-step article for performing ANCOVA in R and Python. This article describes the background of ANCOVA, assumptions, hypotheses, and codes for perform...

## Variable types

Variable types Flowchart for types of variables used for collecting and analyzing the data

## MANOVA using Python (using statsmodels and sklearn)

Code for performing MANOVA in Python

## Manipulated, response, and control variables [definition and research example]

Learn the differences between manipulated, response, and control variable. Manipulated (also known as independent) variable can be changed in the experiment ...

## What is p value and how to calculate p value by hand (with t test example)

Learn how to calculate the p value from t table by hand

## 8 methods to find outliers in R (with examples)

Learn how to detect outlier in the dataset using visual and statistical methods

## Brown-Forsythe test for equality of variances in R

Learn how to perform Brown-Forsythe test for equality of variances in R

## Brown-Forsythe test for equality of means in R

Learn how to perform Brown-Forsythe test for equality of means in R

## ANCOVA code in Python

This article explains how to perform the one-way ANCOVA in Python. You can refer to this article to know more about ANCOVA, when to use ANCOVA, assumptions, ...

## k-means clustering in Python [with example]

Learn how to perform k-means clustering in Python. This article discusses the k-means clustering algorithm, it’s implementation in Python, and visualization ...

## Query pandas DataFrame to select rows based on value and condition matching

Learn how to query pandas DataFrame to select rows based on exact match, partial match, and conditional match in pandas DataFrame

## Import small and large data using pandas (CSV, Excel, Tab, JSON, SQL, and Parquet files)

learn how to import CSV, Excel, Tab, JSON, and SQL files in pandas for data analysis and visualization

## Checking and handling missing values (`NaN`) in pandas

Analyse and handle null or missing values in pandas series and dataframe

## Left, right, outer and inner joins on pandas dataframes

learn to join pandas dataframes in multiple ways

## Violin plot in Python (using seaborn and matplotlib)

Learn how to create violin plots in Python (using seaborn and matplotlib package)

## How to split train and test datasets in Python (using sklearn)

Learn how to split train and test datasets in Python using train_test_split() function from sklearn.model_selection module

## Create a line plot using pandas DataFrame (`pandas.DataFrame.plot.line`)

Create single and multiple line plots from pandas DataFrame. Learn how to use pandas plotting functions for creating grouped line plots.

## Support Vector Machine (SVM) basics and implementation in Python

Implementation of Support vector machine (SVM) in Python for prediction of heart disease. Learn SVM basics, model fitting, model accuracy, and interpretation

## Create scatter plots using Python (matplotlib `pyplot.scatter`)

Learn how to create 2D and 3D scatter plots from numerical arrays and pandas DataFrame using Python matplotlib package

## Linear regression in Python (using sklearn and statsmodels)

A step-by-step article for performing linear regression using statsmodels. This article describes the background of linear regression, types of linear regres...

## Calculating residuals in regression analysis [Manually and with codes]

Learn to calculate residuals in regression analysis manually and with Python and R codes

## DBSCAN in Python (with example dataset)

Learn the basics of DBSCAN and implement DBSCAN clustering in Python

## Multiple ways to select rows, columns, and subsets from pandas DataFrame

This article explains how to select rows, columns, and a subset of pandas DataFrame using various indexing operations and pandas functions

What is pandas?

## How to replace column values in pandas DataFrame based on column conditions

Learn four methods to replace the column values in pandas DataFrame based on column conditions

## How to unpivot pandas DataFrame (wide to long format)

Learn how to convert pandas DataFrame from wide to long format using melt() function

## Pandas groupby function to group column values into list

Group dataframe rows into a list based on a common element from one column

## How to split strings into a list of integers in Python?

Learn how to split the strings as an int list in Python

## How to multiply two or multiple columns in a pandas DataFrame

Learn how to multiply single or multiple columns in a pandas DataFrame

## Calculate harmonic mean in Python (with examples)

Learn what is harmonic mean and how to calculate it in Python

## Generate random dataset with normal distribution in Python (using NumPy)

Learn how to generate a random dataset with normal distribution using NumPy

## How to identify and drop duplicates based on single and multiple columns in a pandas DataFrame

Learn how to identify and drop duplicates in a pandas DataFrame

## Sort dictionary by key and value in Python

Learn how to create and sort Python dictionary by key and value

## Python enumerate to simplify the looping

Python enumerate built-in function allows iterating over list and dictionary and helps to access its items along with index values

## Six ways to get keys from the dictionary in Python

Learn how to obtain keys from dictionary in Python

## Python count() function for strings

Learn how to count strings in Python

## How to add rows to the Pandas DataFrame

Learn various ways to add rows to the Pandas DataFrame

## Python tuples

Python tuples initialization and operations

## 8 different ways to get column names from pandas DataFrame

Learn different methods to get column names from pandas DataFrame

## Simple ways to rename column names in pandas DataFrame

Learn different methods to rename single and multiple column names in pandas DataFrame

## 3 ways to get the last characters of a string in Python

Learn how to get last any number of characters of the strings in Python

## Query pandas DataFrame to split the values in column

Learn how to split the value in pandas DataFrame column and create new columns

## 3 easy ways to remove the last characters of a string in Python

Learn how to get remove any number of characters of the strings in Python

## Perform three types of Z-test in Python (with example dataset)

Learn how to perform one sample, two samples, and paired Z-test in Python. This article also covers when to use Z-test, types of Z-test, assumptions, hypothe...

## Perform three types of t-test in Python

Learn when to use t-test, types of t-test, assumptions, hypothesis, and formula for each type of test, and t-test calculation in Python

## ANOVA using Python (with examples)

One and two-way ANOVA in Python. This article explains ANOVA model, tables, formula, calculation, multiple pairwise comparisons, and results interpretation

## Install and upgrade Python packages using pip, conda, and virtual environment on Windows, Linux, and macOS

Learn how to install, upgrade, and check versions of Python packages

## MANOVA using Python (using statsmodels and sklearn)

Code for performing MANOVA in Python

## ANCOVA code in Python

This article explains how to perform the one-way ANCOVA in Python. You can refer to this article to know more about ANCOVA, when to use ANCOVA, assumptions, ...

## Two-pass alignment of RNA-seq reads with STAR

Complete tutorial on how to use STAR aligner in two-pass mode for mapping RNA-seq reads to genome

## Aligning RNA-seq reads with STAR (Complete tutorial)

Complete tutorial on how to use STAR aligner for mapping RNA-seq reads to genome

## Linux for Bioinformatics (for beginners)

Learn Linux command lines for Bioinformatics analysis

## Survival analysis in R (Kaplan–Meier, Cox proportional hazards, and Log-rank test methods)

Detailed introduction of survival analysis and its calculations in R

## Differential gene expression analysis using edgeR (comprehensive tutorial)

Perform differential gene expression analysis of RNA-seq data using EdgeR

## Differential gene expression analysis using DESeq2 (comprehensive tutorial)

Perform differential gene expression analysis of RNA-seq data using DESeq2

## Create a gene counts matrix from featureCounts

Generate a gene counts matrix when featureCounts run separately on individual aligned files

## Parsing and analyzing BAM files

SAMtools for manipulation of BAM files

## A guide to understanding the variant information fields in variant call format (VCF) file

VCF fields information

## Gene expression units explained: RPM, RPKM, FPKM, TPM, DESeq, TMM, SCnorm, GeTMM, and ComBat-Seq

bulk and single-cell RNA-seq expression units, count normalization, formula, examples in Python, gene quantification, batch effects, and between-sample and w...

## bedtools for genomics analysis

bedtools for comparative analysis of genomic datasets

## t-SNE in Python [single cell RNA-seq example and hyperparameter optimization]

t-SNE using sklearn package. This article explains the basics of t-SNE, differences between t-SNE and PCA, example using scRNA-seq data, and results interpre...

## k-means clustering in Python [with example]

Learn how to perform k-means clustering in Python. This article discusses the k-means clustering algorithm, it’s implementation in Python, and visualization ...

## Sequencing coverage and breadth of coverage

High-through sequencing coverage calculation and coverage recommendations

## pheatmap: create annotated heatmaps in R (detailed guide)

How to create and customize heatmap using pheatmap package in R

## Interactive Heatmap in Python (using hvPlot and Bokeh)

Visualize interactive heatmap using hvPlot and Bokeh

## Heatmap in Python

Heatmap and hierarchical clustering visualization in Python

## Principal component analysis (PCA) and visualization using Python (Detailed guide with example)

PCA using sklearn package. This article explains the basics of PCA, sample size requirement, data standardization, and interpretation of the PCA results

## Volcano plot in Python

Volcano plot using bioinfokit package. This article explains the visualization of volcano plots for gene expression data

## Multiple hypothesis testing problem in Bioinformatics

Multiple hypothesis testing and corrections, type I and II errors, false discovery rate, Bonferroni correction, and Benjamini/Hochberg correction

## Bioinformatics file readers and processing (FASTA, FASTQ, and VCF)

Biological data handling and processing using Python codes

## Manhattan plot in Python

Introduction, analysis, and visualization of Manhattan plot in Python

## MA plot to visualize gene expression data using Python

MA plot basics, analysis, and visualization

## Split the sequence into smaller subsequences

Split the nucleotide sequence into smaller sequences with defined size

## FASTQ Sequence Quality Format

FASTQ sequence example, quality formats, and quality format detection

## Convert GFF3 to GTF file format

Introduction to GFF3 and GTF files, and their interconversions using Python code

## Annotation of genetic variants (SNPs/InDels) in VCF file

Genetic variant annotation for variant location in the genome, associated genes, and their gene functions

## Venn diagrams in Python and R

Create two and three-way Venn diagrams in Python and R

## Reverse complementary

Reverse complementary of DNA sequences

## Concatenate and split VCF files

What is VCF file? VCF stands for variant call format It is a text file (file extension as .vcf) storing meta-information, marker and genotype data of ge...

## Correlation analysis in Python

Correlation analysis using Python code

## pheatmap: create annotated heatmaps in R (detailed guide)

How to create and customize heatmap using pheatmap package in R

## 3 efficient ways to read (import) a CSV file into R

Learn how to read (import) a CSV in R

## Solved: duplicate ‘row.names’ are not allowed error while using `read.csv()`

Solution for how to read a dataset with duplicated row names using read.csv() function

## Calculating residuals in regression analysis [Manually and with codes]

Learn to calculate residuals in regression analysis manually and with Python and R codes

## Calculate harmonic mean in R (with examples)

Learn what is harmonic mean and how to calculate it in R

## How to use `%in%` and `%notin%` operators in R (with examples)

Learn how to use %in% operator in R

## How to use `\$` operator in Data Frame and list in R (with six examples)

Learn how to use \$ operators in R to work with Data Frame and list

## Subset Data Frames in R

Learn to subset or filter Data Frames in R

## How to reorder Data Frame columns by column names and index in R (with examples)

Learn to reorder columns by name and index in R Data Frame

## Perform one sample, two samples, and paired Z-test in R (with example dataset)

Learn when to use Z-test, types of Z-test, assumptions, hypothesis, and formula for each type of test, and Z-test calculation in R

## Fisher’s exact test of independence in R [with post-hoc test]

A step-by-step article for performing Fisher’s exact test in R. This article describes the background of Fisher’s exact test, assumptions, hypotheses, codes,...

## Fisher’s exact test of independence in Python [with example]

A step-by-step article for performing Fisher’s exact test in Python

## How to calculate correlation between two variables in R

This articles explains Pearson’s, Spearman’s rho, and Kendall’s Tau correlation methods and their calculation in R

## Kruskal-Wallis test in R [with example and code]

Kruskal-Wallis test is a non-parametric test for estimating the differences between multiple groups. Learn the basics of Kruskal-Wallis test, its underlying ...

## MANOVA using R (with examples and code)

A step-by-step article for performing MANOVA in R. This article describes the background of MANOVA, assumptions, hypotheses, and codes for performing MANOVA ...

## Friedman test using R (with examples and code)

A step-by-step article for performing Friedman test in R

## Friedman test using Python (with examples and code)

A step-by-step article for performing Friedman test in Python

## ANCOVA using R and Python (with examples and code)

A step-by-step article for performing ANCOVA in R and Python. This article describes the background of ANCOVA, assumptions, hypotheses, and codes for perform...

## 8 methods to find outliers in R (with examples)

Learn how to detect outlier in the dataset using visual and statistical methods

## t-SNE in Python [single cell RNA-seq example and hyperparameter optimization]

t-SNE using sklearn package. This article explains the basics of t-SNE, differences between t-SNE and PCA, example using scRNA-seq data, and results interpre...

## Principal component analysis (PCA) and visualization using Python (Detailed guide with example)

PCA using sklearn package. This article explains the basics of PCA, sample size requirement, data standardization, and interpretation of the PCA results

## Logistic regression in Python (feature selection, model fitting, and prediction)

Logistic regression for prediction of breast cancer, assumptions, feature selection, model fitting, model accuracy, and interpretation

## Decision tree algorithm for classifications (with illustrative example)

Detailed introduction to decision tree learning algorithms and how to construct a decision tree

## Support Vector Machine (SVM) basics and implementation in Python

Implementation of Support vector machine (SVM) in Python for prediction of heart disease. Learn SVM basics, model fitting, model accuracy, and interpretation

## Create scatter plots using Python (matplotlib `pyplot.scatter`)

Learn how to create 2D and 3D scatter plots from numerical arrays and pandas DataFrame using Python matplotlib package

## Multicollinearity and variance inflation factor (VIF) in the regression model (with Python code)

Multicollinearity refers to the significant correlation among the independent variables in the regression model. Variance Inflation Factor (VIF) helps to dia...

## Multiple linear regression (MLR)

Multiple regression analysis using statsmodels. Learn how to define regression model, assumptions, metrics evaluation, and interpretation

## Linear Regression Using Neural Networks (PyTorch)

Linear regression using PyTorch

## Linear regression in Python (using sklearn and statsmodels)

A step-by-step article for performing linear regression using statsmodels. This article describes the background of linear regression, types of linear regres...

## DBSCAN in Python (with example dataset)

Learn the basics of DBSCAN and implement DBSCAN clustering in Python

## Variable types

Variable types Flowchart for types of variables used for collecting and analyzing the data

## 8 methods to find outliers in R (with examples)

Learn how to detect outlier in the dataset using visual and statistical methods

## Query pandas DataFrame to select rows based on value and condition matching

Learn how to query pandas DataFrame to select rows based on exact match, partial match, and conditional match in pandas DataFrame

## Import small and large data using pandas (CSV, Excel, Tab, JSON, SQL, and Parquet files)

learn how to import CSV, Excel, Tab, JSON, and SQL files in pandas for data analysis and visualization

## Checking and handling missing values (`NaN`) in pandas

Analyse and handle null or missing values in pandas series and dataframe

## Left, right, outer and inner joins on pandas dataframes

learn to join pandas dataframes in multiple ways

## Create a line plot using pandas DataFrame (`pandas.DataFrame.plot.line`)

Create single and multiple line plots from pandas DataFrame. Learn how to use pandas plotting functions for creating grouped line plots.

## Multiple ways to select rows, columns, and subsets from pandas DataFrame

This article explains how to select rows, columns, and a subset of pandas DataFrame using various indexing operations and pandas functions

## How to replace column values in pandas DataFrame based on column conditions

Learn four methods to replace the column values in pandas DataFrame based on column conditions

## How to unpivot pandas DataFrame (wide to long format)

Learn how to convert pandas DataFrame from wide to long format using melt() function

## Simple ways to rename column names in pandas DataFrame

Learn different methods to rename single and multiple column names in pandas DataFrame

## Query pandas DataFrame to split the values in column

Learn how to split the value in pandas DataFrame column and create new columns

## Logistic regression in Python (feature selection, model fitting, and prediction)

Logistic regression for prediction of breast cancer, assumptions, feature selection, model fitting, model accuracy, and interpretation

## Multiple linear regression (MLR)

Multiple regression analysis using statsmodels. Learn how to define regression model, assumptions, metrics evaluation, and interpretation

## Linear regression in Python (using sklearn and statsmodels)

A step-by-step article for performing linear regression using statsmodels. This article describes the background of linear regression, types of linear regres...

## ANOVA using Python (with examples)

One and two-way ANOVA in Python. This article explains ANOVA model, tables, formula, calculation, multiple pairwise comparisons, and results interpretation

## ANCOVA using R and Python (with examples and code)

A step-by-step article for performing ANCOVA in R and Python. This article describes the background of ANCOVA, assumptions, hypotheses, and codes for perform...

## k-means clustering in Python [with example]

Learn how to perform k-means clustering in Python. This article discusses the k-means clustering algorithm, it’s implementation in Python, and visualization ...

## Principal component analysis (PCA) and visualization using Python (Detailed guide with example)

PCA using sklearn package. This article explains the basics of PCA, sample size requirement, data standardization, and interpretation of the PCA results

## MANOVA using R (with examples and code)

A step-by-step article for performing MANOVA in R. This article describes the background of MANOVA, assumptions, hypotheses, and codes for performing MANOVA ...

## Bioinformatics file readers and processing (FASTA, FASTQ, and VCF)

Biological data handling and processing using Python codes

## FASTQ Sequence Quality Format

FASTQ sequence example, quality formats, and quality format detection

## Convert GFF3 to GTF file format

Introduction to GFF3 and GTF files, and their interconversions using Python code

## 3 ways to get the last characters of a string in Python

Learn how to get last any number of characters of the strings in Python

## 3 easy ways to remove the last characters of a string in Python

Learn how to get remove any number of characters of the strings in Python

## Linux for Bioinformatics (for beginners)

Learn Linux command lines for Bioinformatics analysis

## k-means clustering in Python [with example]

Learn how to perform k-means clustering in Python. This article discusses the k-means clustering algorithm, it’s implementation in Python, and visualization ...

## DBSCAN in Python (with example dataset)

Learn the basics of DBSCAN and implement DBSCAN clustering in Python

## k-means clustering in Python [with example]

Learn how to perform k-means clustering in Python. This article discusses the k-means clustering algorithm, it’s implementation in Python, and visualization ...

## How to split train and test datasets in Python (using sklearn)

Learn how to split train and test datasets in Python using train_test_split() function from sklearn.model_selection module

## Volcano plot in Python

Volcano plot using bioinfokit package. This article explains the visualization of volcano plots for gene expression data

## Convert GFF3 to GTF file format

Introduction to GFF3 and GTF files, and their interconversions using Python code

## t-SNE in Python [single cell RNA-seq example and hyperparameter optimization]

t-SNE using sklearn package. This article explains the basics of t-SNE, differences between t-SNE and PCA, example using scRNA-seq data, and results interpre...

## Principal component analysis (PCA) and visualization using Python (Detailed guide with example)

PCA using sklearn package. This article explains the basics of PCA, sample size requirement, data standardization, and interpretation of the PCA results

## Kruskal-Wallis test in R [with example and code]

Kruskal-Wallis test is a non-parametric test for estimating the differences between multiple groups. Learn the basics of Kruskal-Wallis test, its underlying ...

## Fisher’s exact test calculator (with formula)

Online calculator for Fisher’s exact test of independence for 2 x 2 contingency table

## How to identify and drop duplicates based on single and multiple columns in a pandas DataFrame

Learn how to identify and drop duplicates in a pandas DataFrame

## Linear Regression Using Neural Networks (PyTorch)

Linear regression using PyTorch

## Linear Regression Using Neural Networks (PyTorch)

Linear regression using PyTorch

## Violin plot in Python (using seaborn and matplotlib)

Learn how to create violin plots in Python (using seaborn and matplotlib package)

## Annotation of genetic variants (SNPs/InDels) in VCF file

Genetic variant annotation for variant location in the genome, associated genes, and their gene functions

## Annotation of genetic variants (SNPs/InDels) in VCF file

Genetic variant annotation for variant location in the genome, associated genes, and their gene functions