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
Complete tutorial on how to use STAR aligner in two-pass mode for mapping RNA-seq reads to genome
Complete tutorial on how to use STAR aligner for mapping RNA-seq reads to genome
Learn Linux command lines for Bioinformatics analysis
Detailed introduction of survival analysis and its calculations in R
Perform differential gene expression analysis of RNA-seq data using EdgeR
Perform differential gene expression analysis of RNA-seq data using DESeq2
Generate a gene counts matrix when featureCounts run separately on individual aligned files
SAMtools for manipulation of BAM files
NCBI E-utilities for downloading the single or large number of sequences from the NCBI sequence database
VCF fields information
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 comparative analysis of genomic datasets
Downloading FASTQ files from NCBI SRA database
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...
Learn how to perform k-means clustering in Python. This article discusses the k-means clustering algorithm, it’s implementation in Python, and visualization ...
High-through sequencing coverage calculation and coverage recommendations
How to create and customize heatmap using pheatmap package in R
Visualize interactive heatmap using hvPlot and Bokeh
Heatmap and hierarchical clustering visualization in Python
PCA using sklearn package. This article explains the basics of PCA, sample size requirement, data standardization, and interpretation of the PCA results
Volcano plot using bioinfokit package. This article explains the visualization of volcano plots for gene expression data
Multiple hypothesis testing and corrections, type I and II errors, false discovery rate, Bonferroni correction, and Benjamini/Hochberg correction
Biological data handling and processing using Python codes
Introduction, analysis, and visualization of Manhattan plot in Python
MA plot basics, analysis, and visualization
Split the nucleotide sequence into smaller sequences with defined size
FASTQ sequence example, quality formats, and quality format detection
Introduction to GFF3 and GTF files, and their interconversions using Python code
FASTQ to FASTA, GFF3 to GTF, HMM to CSV, TAB to CSV, and CSV to TAB
Genetic variant annotation for variant location in the genome, associated genes, and their gene functions
Learn how to propose null and Alternative hypotheses, perform the statistical analysis, and interpret the results
Learn how to read (import) a CSV in R
Solution for how to read a dataset with duplicated row names using read.csv() function
Learn how to query pandas DataFrame to select rows based on exact match, partial match, and conditional match in pandas DataFrame
learn how to import CSV, Excel, Tab, JSON, and SQL files in pandas for data analysis and visualization
NaN) in pandas
Analyse and handle null or missing values in pandas series and dataframe
learn to join pandas dataframes in multiple ways
Learn how to use probability distributions, probability mass function (PMF), cumulative distribution function (CDF), and probability density function (PDF)
Logistic regression for prediction of breast cancer, assumptions, feature selection, model fitting, model accuracy, and interpretation
Learn how to create violin plots in Python (using seaborn and matplotlib package)
Learn how to split train and test datasets in Python using train_test_split() function from sklearn.model_selection module
This article explains how to create scatter plots using pandas DataFrame
Create single and multiple line plots from pandas DataFrame. Learn how to use pandas plotting functions for creating grouped line plots.
Detailed introduction to decision tree learning algorithms and how to construct a decision tree
Implementation of Support vector machine (SVM) in Python for prediction of heart disease. Learn SVM basics, model fitting, model accuracy, and interpretation
Learn how to create 2D and 3D scatter plots from numerical arrays and pandas DataFrame using Python matplotlib package
Multicollinearity refers to the significant correlation among the independent variables in the regression model. Variance Inflation Factor (VIF) helps to dia...
Multiple regression analysis using statsmodels. Learn how to define regression model, assumptions, metrics evaluation, and interpretation
Linear regression using PyTorch
A step-by-step article for performing linear regression using statsmodels. This article describes the background of linear regression, types of linear regres...
Learn to calculate residuals in regression analysis manually and with Python and R codes
Learn the basics of DBSCAN and implement DBSCAN clustering in Python
This article explains how to select rows, columns, and a subset of pandas DataFrame using various indexing operations and pandas functions
What is pandas?
Learn four methods to replace the column values in pandas DataFrame based on column conditions
Learn how to convert pandas DataFrame from wide to long format using melt() function
Group dataframe rows into a list based on a common element from one column
Learn how to split the strings as an int list in Python
Learn how to setup a passwordless login to remote SSH server
Learn how to multiply single or multiple columns in a pandas DataFrame
Learn what is harmonic mean and how to calculate it in R
Learn what is harmonic mean and how to calculate it in Python
Learn how to generate a random dataset with normal distribution using NumPy
Learn how to identify and drop duplicates in a pandas DataFrame
Learn how to create and sort Python dictionary by key and value
Python enumerate built-in function allows iterating over list and dictionary and helps to access its items along with index values
Learn how to obtain keys from dictionary in Python
Learn how to count strings in Python
Learn various ways to add rows to the Pandas DataFrame
Python tuples initialization and operations
%notin%operators in R (with examples)
Learn how to use %in% operator in R
$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
Learn different methods to get column names from pandas DataFrame
Learn to subset or filter Data Frames in R
Learn to reorder columns by name and index in R Data Frame
Learn different methods to rename single and multiple column names in pandas DataFrame
Learn how to get last any number of characters of the strings in Python
Learn how to split the value in pandas DataFrame column and create new columns
Learn how to get remove any number of characters of the strings in Python
Learn when to use and how to calculate Chi-squared test for independence
Create two and three-way Venn diagrams in Python and R
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
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...
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
Learn to perform sample proportions Z-Test in R
Learn when to use Mann-Whitney U test, assumptions, hypothesis, and formula, and test calculation in Python
Calculate Mann-Whitney U test online calculator
Learn to perform Durbin-Watson test (a test for autocorrelation) in R
Learn to perform Durbin-Watson test (a test for autocorrelation) in Python
Calculate three types of t-test from scratch
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,...
A step-by-step article for performing Fisher’s exact test in Python
Online calculator for Fisher’s exact test of independence for 2 x 2 contingency table
Reverse complementary of DNA sequences
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...
This articles explains Pearson’s, Spearman’s rho, and Kendall’s Tau correlation methods and their calculation in R
Correlation analysis using Python code
Repeated Measure ANOVA in Python and R. This article explains repeated Measure ANOVA model, multiple pairwise comparisons, and results interpretation
Learn to perform mixed ANOVA, check assumptions, and post-hoc tests for significant interactions and main effects
Kruskal-Wallis test is a non-parametric test for estimating the differences between multiple groups. Learn the basics of Kruskal-Wallis test, its underlying ...
One and two-way ANOVA in Python. This article explains ANOVA model, tables, formula, calculation, multiple pairwise comparisons, and results interpretation
Learn how to install, upgrade, and check versions of Python packages
A step-by-step article for performing MANOVA in R. This article describes the background of MANOVA, assumptions, hypotheses, and codes for performing MANOVA ...
A step-by-step article for performing Friedman test in R
A step-by-step article for performing Friedman test in Python
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...
Title: Advanced Bioinformatics Workshop
Learn how to perform stratified sampling with example in Python
Learn how to perform random sampling with and without replacement and example in Python
Variable types Flowchart for types of variables used for collecting and analyzing the data
Code for performing MANOVA in Python
Learn the differences between manipulated, response, and control variable. Manipulated (also known as independent) variable can be changed in the experiment ...
Learn how to calculate the p value from t table by hand
Learn how to detect outlier in the dataset using visual and statistical methods
Learn how to perform Brown-Forsythe test for equality of variances in R
Learn how to perform Brown-Forsythe test for equality of means in R
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, ...