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
2022
Aligning RNA-seq reads with STAR (Complete tutorial)
Complete tutorial on how to use STAR aligner for mapping RNA-seq reads to genome
2021
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
Entrez programming utilities for downloading the nucleotide and protein sequences from NCBI
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
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
How to use NCBI SRA Toolkit effectively?
Downloading FASTQ files from NCBI SRA database
t-SNE in Python for visualization of high-dimensional data
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
File format conversions
FASTQ to FASTA, GFF3 to GTF, HMM to CSV, TAB to CSV, and CSV to TAB
Annotation of genetic variants (SNPs/InDels) in VCF file
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
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
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
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
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)
2020
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
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 scatter plot using pandas DataFrame (pandas.DataFrame.plot.scatter)
This article explains how to create scatter plots using pandas DataFrame
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.
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...
Calculating residuals in regression analysis [Manually and with codes]
Learn to calculate residuals in regression analysis manually and with Python and R codes
DBSCAN clustering algorithm 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
Data handling and manipulation with Pandas
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 setup passwordless login to the SSH server
Learn how to setup a passwordless login to remote SSH server
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 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 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
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
8 different ways to get column names from pandas DataFrame
Learn different methods to get column names from pandas DataFrame
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
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
2019
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
Venn diagrams in Python and R
Create two and three-way Venn diagrams in Python and R
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
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...
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
2018
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
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 ...
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 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...
2017
Advanced Bioinformatics Workshop
Title: Advanced Bioinformatics Workshop
2016
What is Stratified sampling and why should you use it (with example in Python)?
Learn how to perform stratified sampling with example in Python
Understanding random sampling with and without replacement (with python code)
Learn how to perform random sampling with and without replacement and example in Python
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, ...
