Blog articles

2024 9
2023 59
2022 2
2021 37
2020 41
2019 18
2018 9
2017 1
2016 10

2024

Calculate Coverage From BAM File

2 minute read

Learn how to use samtools depth and coverage commands to calculate the coverage from BAM file

Python: Why VIF Return Inf Value?

3 minute read

Learn resons behind the Inf Value in VIF analysis in Python with example

Find Max and Min Sequence Length in Fasta

1 minute read

Learn how to find the maximum and minimum sequence lengths in a FASTA file using Python, seqkit, and samtools

Get Non-overlapping Portion Between Two Regions in bedtools

2 minute read

Learn how to use bedtools subtract to get non-overlapping portion between two regions in BED files

What is Log2 Fold Change in Bioinformatics

2 minute read

Learn what is log2 fold change, how to calculate log2 fold change, and why log2 transformation used for measuring the fold change between samples in bioinfo...

Samtools: Extract Reads from Specific Genomic Regions

2 minute read

Learn how to extract reads from BAM files that fall within a specified region with samtools

Samtools: Extract Mapped and Unmapped Paired-end Reads

2 minute read

Learn how to filter mapped and unmapped paired-end reads with Samtools

Samtools: How to Filter Mapped and Unmapped Reads

2 minute read

Learn how to filter mapped and unmapped sequence reads with Samtools

What is Singleton in Bioinformatics?

1 minute read

This tutorial explains what is singleton in bioinformatics

2023

How to Create Histogram Using NumPy

2 minute read

Learn how to Generate a histogram with NumPy

How to Calculate Antilog of Values in R

2 minute read

Learn how to calculate antilogarithms in R common and natural logarithms with practical examples

How to Calculate Antilog of Values in Python

2 minute read

Learn how to calculate antilogarithms in Python common and natural logarithms with practical examples

Quantile vs Percentile in Python

2 minute read

Learn the key differences between quantiles and percentiles in Python

Difference Between Quantile, Quartile, and Percentile

3 minute read

Learn the distinctions between quantiles, quartiles, and percentiles in statistics. Understand how these metrics divide and analyze data, providing insights ...

Kaplan-Meier Survival Analysis in R

3 minute read

Learn how to visualize and analyze survival times, compare groups, and assess the impact of predictor variables using Kaplan-Meier curves in R

ComplexHeatmap: Create Complex Heatmaps in R

2 minute read

Learn how to create customized heatmaps using ComplexHeatmap in R

Calculate Quartiles in R

2 minute read

Learn how to calculate and visualize quartiles in R

`random.uniform()`: R `runif()` Equivalent Function in Python

2 minute read

Learn how to use random.uniform(): Python counterpart to R’s runif() function

Calculate Quartiles in Python

2 minute read

Learn how to calculate quartiles in Python using NumPy and pandas

Calculate AUC in Python (With Example)

2 minute read

Learn how to compute AUC (Area Under the Curve) in Python for evaluating classification model performance

Calculate AUC in R: Step-by-Step Guide With Example

2 minute read

Learn how to compute AUC (Area Under the Curve) in R for evaluating classification model performance

Two-sample Kolmogorov-Smirnov test in R

2 minute read

Comprehensive guide to the two-sample Kolmogorov-Smirnov test in R

How to Plot ROC Curve in R

2 minute read

Learn how to plot ROC curve in R for model evaluation

How to Plot ROC Curve in Python

3 minute read

Learn how to plot ROC curve in Python for model evaluation

Q-Q plot in Python

1 minute read

Learn how to create a Q-Q plot in Python to assess the normal distribution of the data

One-sample Kolmogorov-Smirnov test in R

2 minute read

Comprehensive guide to the One-sample Kolmogorov-Smirnov test in R

How to Use runif in R (Practical Examples)

3 minute read

Learn how to generate random numbers from uniform distributions in R with the runif() function

Binary Logistic Regression in R

5 minute read

Learn how to perform binary logistic regression in R and evaluate the model performance

How to Use bedtools merge

2 minute read

Learn bedtools merge for combining overlapping and adjacent intervals in the BED file

How to Use bedtools intersect

4 minute read

Learn bedtools intersect for finding overlapping and non-overlapping intervals between BED files in various ways

Calculate All Possible Combinations of DNA bases

1 minute read

Calculate all DNA base combinations with Python code

Shapiro–Wilk Test in R

2 minute read

Learn to perform the Shapiro-Wilk test for normality in R with step-by-step guidance and make sure the data meets the normality assumption for reliable stati...

Q-Q plot in R

2 minute read

Learn how to create a Q-Q plot in R to assess the normal distribution of the data

How to Perform Mann-Whitney U test in R

3 minute read

Learn how to conduct the Mann-Whitney U test in R for non-parametric group comparison

Steps in PCR

2 minute read

Learn the step-by-step process of Polymerase Chain Reaction (PCR)

Methods to Calculate Melting Temperature (Tm) for Primers

2 minute read

Learn how to calculate primer melting temperature (Tm) for precise DNA amplification and molecular biology experiments

Calculate Melting Temperature (Tm) in R

2 minute read

Three methods to calculate melting temperature (Tm) in R

Calculate Melting Temperature (Tm) in Python

1 minute read

Three methods to calculate melting temperature (Tm) in Python

Understanding E-value, bit score, and p value in BLAST

3 minute read

Explore the significance of E-value, bit score, and p-value in BLAST alignments. Gain insights into how these parameters assess homology between biological s...

How to Use `seqtk subseq` to Extract Sequences from FASTA/FASTQ Files

3 minute read

Learn seqtk subseq function for extracting specific sequences and subsequences from a FASTA/FASTQ files

Convert Multi-line Fasta into Single-line Fasta

1 minute read

Convert Multi-line Fasta into Single-line Fasta using Python

How to Extract Sequences from FASTA in Python

2 minute read

Learn extract_seq() from bioinfokit function for extracting specific sequences and subsequences from a FASTA file

How to Count Number of Columns in CSV File in Bash

less than 1 minute read

Learn how to count the number of columns in a CSV file using awk

`blastp`: Command-line Utility for Protein Sequence Search

3 minute read

Perform protein sequence similarity searches with the blastp command-line tool

`blastn` vs `blastp`: Which One You Should Use?

1 minute read

What is difference between blastn and blastp

`blastn`: Command-line Utility for Nucleotide Sequence Search

3 minute read

Perform Nucleotide sequence similarity searches with the blastn command-line tool

How to Use `blastdbcmd` to Extract Sequences from BLAST Database

1 minute read

blastdbcmd: A command-line tool for retrieving all or specific sequences from formatted BLAST databases

How to Reverse Complement of DNA Sequence in Python

1 minute read

Get the reverse complement of a DNA sequence in a Python

How to Reverse Complement of DNA Sequence in Bash

1 minute read

Get the reverse complement of a DNA sequence in a one-liner Bash command using awk, tr, and rev

Create a Local BLAST Database From FASTA File

2 minute read

Creating a local BLAST database from FASTA file for faster, customized sequence similarity searches

Two-Way ANOVA in R: How to Analyze and Interpret Results

4 minute read

This article explains how to perform two-way ANOVA in R

How to Perform One-Way ANOVA in R (With Example Dataset)

3 minute read

This article explains how to perform one-way ANOVA in R

What is Nextflow and How to Use it?

1 minute read

Learn what is Nextflow and how to use it for running bioinformatics pipeline

Convert FASTQ to FASTA Format

2 minute read

List of Bioinformatics tools to convert FASTQ file into FASTA format

Canu: Genome Assembly for PacBio and Nanopore Long-Reads (Detailed Guide)

3 minute read

Assemble PacBio and Nanopore long-reads using the Canu

IUPAC Nucleotide Codes

1 minute read

IUPAC codes for representing nucleotide degeneracy

How to Use bedtools getfasta to Extract DNA Sequences (With Example)

3 minute read

This article describes how to use the bedtools getfasta command to extract the sequence from the FASTA file based on the genomic coordinates given in the B...

How to Determine Strandedness in RNA-seq Data (With Example)

3 minute read

Determine strandedness in RNA-seq using RSeQC quality control tool

What is Strandedness in RNA-seq?

1 minute read

RNA-seq strandedness and difference between stranded and non-stranded RNA-seq

How to Calculate Descriptive Statistics in Python with Pandas DataFrame

3 minute read

Calculate descriptive statistics using describe() function from pandas DataFrame

How to Use `describe()` Function in R

2 minute read

learn how to use describe() function in R with several examples

How to Compute Trimmed Mean in R?

4 minute read

Learn how to calculate trimmed mean in R with several examples

`summary()` Function in R: How to Use (With 6 Examples)?

4 minute read

How to use summary() function in R to get summarise the fitted model results

HISAT2: Fast Aligner for NGS Data (complete Tutorial)

6 minute read

This tutorial explains how to use HISAT2 for aligning NGS reads to genome

How to Get R-Squared and Adjusted R-Squared From `lm` in R

2 minute read

Extract R-Squared and adjusted R-Squared from lm summary statistics after fitting regression model

How to Get F Statistics and p Value From `lm` in R

2 minute read

Extract F Statistics and p value from lm summary statistics after fitting regression model

How to Calculate VIF in R

4 minute read

This article describes how to calculate the Variance Inflation Factor (VIF) to detect multicollinearity in R

Covariate in Statistics: Definition and Examples

3 minute read

Explanation of covariate in statistics, covariate examples, and how to use covariate in statistical analysis

2022

Two-pass alignment of RNA-seq reads with STAR

4 minute read

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

Mastering RNA-seq Read Alignment With STAR

8 minute read

Learn how to align RNA-seq reads with STAR for accurate gene expression analysis in bioinformatics

2021

Linux for Bioinformatics (for beginners)

15 minute read

Learn Linux command lines for Bioinformatics analysis

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

6 minute read

Detailed introduction of survival analysis and its calculations in R

RNA-seq Data Analysis with edgeR

8 minute read

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

RNA-seq Data Analysis with DESeq2

9 minute read

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

Create a gene counts matrix from featureCounts

1 minute read

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

Parsing and analyzing BAM files

6 minute read

SAMtools for manipulation of BAM files

How to Use E-utilities for Downloading Sequences from NCBI

5 minute read

NCBI E-utilities for downloading the single or large number of sequences from the NCBI sequence database

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

6 minute read

VCF fields information

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

15 minute read

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

8 minute read

bedtools for comparative analysis of genomic datasets

How to use NCBI SRA Toolkit effectively?

6 minute read

Downloading FASTQ files from NCBI SRA database

UMAP dimension reduction algorithm in Python (with example)

6 minute read

How to reduce and visualize high-dimensional data using UMAP in Python

t-SNE in Python for visualization of high-dimensional data

8 minute read

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: Detailed Guide With Example

8 minute read

This article how to perform and visualize the K-means Clustering in Python

Sequencing coverage and breadth of coverage

4 minute read

High-through sequencing coverage calculation and coverage recommendations

pheatmap: create annotated heatmaps in R (detailed guide)

5 minute read

How to create and customize heatmap using pheatmap package in R

Interactive Heatmap in Python (using hvPlot and Bokeh)

1 minute read

Visualize interactive heatmap using hvPlot and Bokeh

Heatmap in Python

3 minute read

Heatmap and hierarchical clustering visualization in Python

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

11 minute read

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

4 minute read

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

Multiple hypothesis testing problem in Bioinformatics

5 minute read

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)

1 minute read

Biological data handling and processing using Python codes

Manhattan plot in Python

3 minute read

Introduction, analysis, and visualization of Manhattan plot in Python

MA plot to visualize gene expression data using Python

3 minute read

MA plot basics, analysis, and visualization

Split the sequence into smaller subsequences

less than 1 minute read

Split the nucleotide sequence into smaller sequences with defined size

FASTQ Sequence Quality Format

2 minute read

FASTQ sequence example, quality formats, and quality format detection

Convert GFF3 to GTF file format

5 minute read

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

File format conversions

less than 1 minute read

GFF3 to GTF, HMM to CSV, TAB to CSV, and CSV to TAB

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

3 minute read

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

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

4 minute read

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

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

5 minute read

Learn how to read (import) a CSV in R

Solving the Most Common R Error: ‘Duplicate row.names are not allowed’

2 minute read

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

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

3 minute read

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)

5 minute read

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

4 minute read

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

Left, right, outer and inner joins on pandas dataframes

1 minute read

learn to join pandas dataframes in multiple ways

Find probabilities using discrete and continuous probability distributions

2 minute read

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

2020

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

9 minute read

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

Violin plot in Python (using seaborn and matplotlib)

4 minute read

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

How to Split Data into Train and Test Sets in Python with sklearn

4 minute read

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

Create a scatter plot using pandas DataFrame (`pandas.DataFrame.plot.scatter`)

3 minute read

This article explains how to create scatter plots using pandas DataFrame

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

4 minute read

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

Decision tree algorithm for classifications (with illustrative example)

8 minute read

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

Support Vector Machine (SVM) in Python

7 minute read

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`)

4 minute read

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)

4 minute read

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)

8 minute read

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

Linear Regression Using Neural Networks (PyTorch)

5 minute read

Linear regression using PyTorch

Linear regression in Python (using sklearn and statsmodels)

6 minute read

This article explains background of the linear regression and how to perform a linear regression with a Python code.

Calculating residuals in regression analysis [Manually and with codes]

5 minute read

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

DBSCAN clustering algorithm in Python (with example dataset)

7 minute read

Learn the basics of DBSCAN and implement DBSCAN clustering in Python

How to subset from pandas DataFrame?

5 minute read

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

Data handling and manipulation with Pandas

13 minute read

What is pandas?

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

4 minute read

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

How to unpivot pandas DataFrame (wide to long format)

3 minute read

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

Pandas groupby function to group column values into list

1 minute read

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?

2 minute read

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

How to setup passwordless login to the SSH server

3 minute read

Learn how to setup a passwordless login to remote SSH server

How to multiply two or multiple columns in a pandas DataFrame

3 minute read

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

Calculate harmonic mean in R (with examples)

1 minute read

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

Calculate harmonic mean in Python (with examples)

1 minute read

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

Generate dataset with normal distribution in Python

2 minute read

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

4 minute read

Learn how to identify and drop duplicates in a pandas DataFrame

Sort dictionary by key and value in Python

2 minute read

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

Python enumerate to simplify the looping

2 minute read

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

1 minute read

Learn how to obtain keys from dictionary in Python

Python count() function for strings

1 minute read

Learn how to count strings in Python

How to add rows to the Pandas DataFrame

2 minute read

Learn various ways to add rows to the Pandas DataFrame

Python tuples

2 minute read

Python tuples initialization and operations

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

8 minute read

Learn how to use %in% operator in R

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

3 minute read

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

8 different ways to get column names from pandas DataFrame

1 minute read

Learn different methods to get column names from pandas DataFrame

Subset Data Frames in R

2 minute read

Learn to subset or filter Data Frames in R

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

2 minute read

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

Simple ways to rename column names in pandas DataFrame

2 minute read

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

1 minute read

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

Query pandas DataFrame to split the values in column

1 minute read

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

1 minute read

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

2019

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

4 minute read

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

Venn diagrams in Python and R

1 minute read

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

Analyze one and two-sample Z-test in R

5 minute read

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

Mastering Z-test in Python: A Step-by-Step Guide (With Examples)

9 minute read

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...

How to perform one and two-sample t-test in Python

9 minute read

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)

6 minute read

Learn to perform sample proportions Z-Test in R

How to Perform Mann-Whitney U test in Python

5 minute read

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)

less than 1 minute read

Calculate Mann-Whitney U test online calculator

How to Conduct Durbin-Watson Test in R

4 minute read

Find out how to detect autocorrelation in your data using the Durbin-Watson test in R. Get a step-by-step guide on how to run this test.

Perform Durbin-Watson (DW) test in Python

2 minute read

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

Perform t-test from scratch in Python

3 minute read

Calculate three types of t-test from scratch

How to Perform Fisher’s Exact Test in R

5 minute read

Learn Conduct Fisher exact test in R for categorical data associations

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

2 minute read

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

Fisher’s exact test calculator (with formula)

less than 1 minute read

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

Reverse Complement of DNA Sequences

less than 1 minute read

Reverse complementary of DNA sequences

Concatenate and split VCF files

1 minute read

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...

How to calculate correlation between two variables in R

5 minute read

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

Correlation analysis in Python

2 minute read

Correlation analysis using Python code

2018

Repeated Measures ANOVA using Python and R (with examples)

7 minute read

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)

5 minute read

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

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

6 minute read

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

How to Perform ANOVA in Python

16 minute read

Learn how to conduct one-way and two-way ANOVA tests, interpret results, and make informed statistical decisions using Python

pip and conda to install and upgrade Python packages

5 minute read

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

How to Perform MANOVA in R

9 minute read

Learn how to conduct Multivariate Analysis of Variance (MANOVA) in R with step-by-step guidance

Friedman test using R (with examples and code)

5 minute read

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

Friedman test using Python (with examples and code)

3 minute read

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

ANCOVA using R and Python (with examples and code)

8 minute read

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...

2017

Advanced Bioinformatics Workshop

less than 1 minute read

Title: Advanced Bioinformatics Workshop