How to Use bedtools merge
Learn bedtools merge for combining overlapping and adjacent intervals in the BED file
Learn bedtools merge for combining overlapping and adjacent intervals in the BED file
Learn bedtools intersect for finding overlapping and non-overlapping intervals between BED files in various ways
Calculate all DNA base combinations with Python code
Learn the step-by-step process of Polymerase Chain Reaction (PCR)
Learn how to calculate primer melting temperature (Tm) for precise DNA amplification and molecular biology experiments
Three methods to calculate melting temperature (Tm) in R
Three methods to calculate melting temperature (Tm) in Python
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...
seqtk subseq
to Extract Sequences from FASTA/FASTQ Files
Learn seqtk subseq function for extracting specific sequences and subsequences from a FASTA/FASTQ files
Convert Multi-line Fasta into Single-line Fasta using Python
Learn extract_seq() from bioinfokit function for extracting specific sequences and subsequences from a FASTA file
blastp
: Command-line Utility for Protein Sequence Search
Perform protein sequence similarity searches with the blastp command-line tool
blastn
vs blastp
: Which One You Should Use?
What is difference between blastn and blastp
blastn
: Command-line Utility for Nucleotide Sequence Search
Perform Nucleotide sequence similarity searches with the blastn command-line tool
blastdbcmd
to Extract Sequences from BLAST Database
blastdbcmd: A command-line tool for retrieving all or specific sequences from formatted BLAST databases
Get the reverse complement of a DNA sequence in a Python
Get the reverse complement of a DNA sequence in a one-liner Bash command using awk, tr, and rev
Creating a local BLAST database from FASTA file for faster, customized sequence similarity searches
Learn what is Nextflow and how to use it for running bioinformatics pipeline
List of Bioinformatics tools to convert FASTQ file into FASTA format
Assemble PacBio and Nanopore long-reads using the Canu
IUPAC codes for representing nucleotide degeneracy
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...
Determine strandedness in RNA-seq using RSeQC quality control tool
RNA-seq strandedness and difference between stranded and non-stranded RNA-seq
This tutorial explains how to use HISAT2 for aligning NGS reads to genome
Complete tutorial on how to use STAR aligner in two-pass mode for mapping RNA-seq reads to genome
Learn how to align RNA-seq reads with STAR for accurate gene expression analysis in bioinformatics
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
How to reduce and visualize high-dimensional data using UMAP in Python
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...
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
Genetic variant annotation for variant location in the genome, associated genes, and their gene functions
Create two and three-way Venn diagrams in Python and R
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...
Correlation analysis using Python code
Title: Advanced Bioinformatics Workshop
Comprehensive guide to the two-sample Kolmogorov-Smirnov test in R
Learn how to create a Q-Q plot in Python to assess the normal distribution of the data
Comprehensive guide to the One-sample Kolmogorov-Smirnov test in R
Learn how to perform binary logistic regression in R and evaluate the model performance
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...
Learn how to create a Q-Q plot in R to assess the normal distribution of the data
Learn how to conduct the Mann-Whitney U test in R for non-parametric group comparison
This article explains how to perform two-way ANOVA in R
This article explains how to perform one-way ANOVA in R
Calculate descriptive statistics using describe() function from pandas DataFrame
describe()
Function in R
learn how to use describe() function in R with several examples
Learn how to calculate trimmed mean in R with several examples
summary()
Function in R: How to Use (With 6 Examples)?
How to use summary() function in R to get summarise the fitted model results
lm
in R
Extract R-Squared and adjusted R-Squared from lm summary statistics after fitting regression model
lm
in R
Extract F Statistics and p value from lm summary statistics after fitting regression model
This article describes how to calculate the Variance Inflation Factor (VIF) to detect multicollinearity in R
Explanation of covariate in statistics, covariate examples, and how to use covariate in statistical analysis
Multiple hypothesis testing and corrections, type I and II errors, false discovery rate, Bonferroni correction, and Benjamini/Hochberg correction
Learn how to propose null and Alternative hypotheses, perform the statistical analysis, and interpret the results
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
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
Learn to calculate residuals in regression analysis manually and with Python and R codes
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 when to use and how to calculate Chi-squared test for independence
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
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.
Learn to perform Durbin-Watson test (a test for autocorrelation) in Python
Calculate three types of t-test from scratch
Learn how to perform Fisher’s exact test of independence in R
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
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
One and two-way ANOVA in Python. This article explains ANOVA model, tables, formula, calculation, multiple pairwise comparisons, and results interpretation
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...
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 p-values by hand (using t test example) to gain a deeper understanding of statistical hypothesis testing.
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, ...
Learn how to create a Q-Q plot in Python to assess the normal distribution of the data
Calculate descriptive statistics using describe() function from pandas DataFrame
This article how to perform and visualize the K-means Clustering in Python
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 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
pandas.DataFrame.plot.scatter
)
This article explains how to create scatter plots 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.
Implementation of Support vector machine (SVM) in Python for prediction of heart disease. Learn SVM basics, model fitting, model accuracy, and interpretation
pyplot.scatter
)
Learn how to create 2D and 3D scatter plots from numerical arrays and pandas DataFrame using Python matplotlib package
This article explains background of the linear regression and how to perform a linear regression with a Python code.
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 multiply single or multiple columns in a pandas DataFrame
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
Learn different methods to get column names from pandas DataFrame
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 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
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
Code for performing MANOVA 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, ...
Learn how to compute AUC (Area Under the Curve) in R for evaluating classification model performance
Comprehensive guide to the two-sample Kolmogorov-Smirnov test in R
Learn how to plot ROC curve in R for model evaluation
Comprehensive guide to the One-sample Kolmogorov-Smirnov test in R
Learn how to perform binary logistic regression in R and evaluate the model performance
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...
Learn how to create a Q-Q plot in R to assess the normal distribution of the data
Learn how to conduct the Mann-Whitney U test in R for non-parametric group comparison
This article explains how to perform two-way ANOVA in R
This article explains how to perform one-way ANOVA in R
describe()
Function in R
learn how to use describe() function in R with several examples
Learn how to calculate trimmed mean in R with several examples
summary()
Function in R: How to Use (With 6 Examples)?
How to use summary() function in R to get summarise the fitted model results
lm
in R
Extract R-Squared and adjusted R-Squared from lm summary statistics after fitting regression model
lm
in R
Extract F Statistics and p value from lm summary statistics after fitting regression model
This article describes how to calculate the Variance Inflation Factor (VIF) to detect multicollinearity in R
How to create and customize heatmap using pheatmap package in R
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 to calculate residuals in regression analysis manually and with Python and R codes
Learn what is harmonic mean and how to calculate it in R
%in%
and %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 to subset or filter Data Frames in R
Learn to reorder columns by name and index in R Data Frame
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 Fisher’s exact test of independence in R
A step-by-step article for performing Fisher’s exact test in Python
This articles explains Pearson’s, Spearman’s rho, and Kendall’s Tau correlation methods and their calculation in R
Kruskal-Wallis test is a non-parametric test for estimating the differences between multiple groups. Learn the basics of Kruskal-Wallis test, its underlying ...
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...
Learn how to detect outlier in the dataset using visual and statistical methods
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
pandas.DataFrame.plot.scatter
)
This article explains how to create scatter plots 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.
This article explains how to select rows, columns, and a subset of pandas DataFrame using various indexing operations and pandas functions
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
Learn different methods to rename single and multiple column names in pandas DataFrame
Learn how to split the value in pandas DataFrame column and create new columns
PCA using sklearn package. This article explains the basics of PCA, sample size requirement, data standardization, and interpretation of the PCA results
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
pyplot.scatter
)
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
This article explains background of the linear regression and how to perform a linear regression with a Python code.
Learn the basics of DBSCAN and implement DBSCAN clustering in Python
Variable types Flowchart for types of variables used for collecting and analyzing the data
Learn how to detect outlier in the dataset using visual and statistical methods
How to reduce and visualize high-dimensional data using UMAP in Python
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...
This article how to perform and visualize the K-means Clustering in Python
Learn how to split train and test datasets in Python using train_test_split() function from sklearn.model_selection module
Learn how to perform stratified sampling with example in Python
Learn how to perform random sampling with and without replacement and example in Python
Logistic regression for prediction of breast cancer, assumptions, feature selection, model fitting, model accuracy, and interpretation
Multiple regression analysis using statsmodels. Learn how to define regression model, assumptions, metrics evaluation, and interpretation
This article explains background of the linear regression and how to perform a linear regression with a Python code.
One and two-way ANOVA in Python. This article explains ANOVA model, tables, formula, calculation, multiple pairwise comparisons, and results interpretation
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...
Learn how to compute AUC (Area Under the Curve) in R for evaluating classification model performance
Learn how to plot ROC curve in R for model evaluation
Learn how to perform binary logistic regression in R and evaluate the model performance
Logistic regression for prediction of breast cancer, assumptions, feature selection, model fitting, model accuracy, and interpretation
Linear regression using PyTorch
Learn how to count the number of columns in a CSV file using awk
Learn Linux command lines for Bioinformatics analysis
Learn how to setup a passwordless login to remote SSH server
Biological data handling and processing using Python codes
FASTQ sequence example, quality formats, and quality format detection
Introduction to GFF3 and GTF files, and their interconversions using Python code
How to reduce and visualize high-dimensional data using UMAP in Python
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...
PCA using sklearn package. This article explains the basics of PCA, sample size requirement, data standardization, and interpretation of the PCA results
Learn the step-by-step process of Polymerase Chain Reaction (PCR)
Learn how to calculate primer melting temperature (Tm) for precise DNA amplification and molecular biology experiments
Three methods to calculate melting temperature (Tm) in R
PCA using sklearn package. This article explains the basics of PCA, sample size requirement, data standardization, and interpretation of the PCA results
A step-by-step article for performing MANOVA in R. This article describes the background of MANOVA, assumptions, hypotheses, and codes for performing MANOVA ...
Learn how to get last any number of characters of the strings in Python
Learn how to get remove any number of characters of the strings in Python
Volcano plot using bioinfokit package. This article explains the visualization of volcano plots for gene expression data
Introduction to GFF3 and GTF files, and their interconversions using Python 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 ...
Online calculator for Fisher’s exact test of independence for 2 x 2 contingency table
Learn how to identify and drop duplicates in a pandas DataFrame
Learn how to create violin plots in Python (using seaborn and matplotlib package)
Genetic variant annotation for variant location in the genome, associated genes, and their gene functions
Genetic variant annotation for variant location in the genome, associated genes, and their gene functions
Introduction, analysis, and visualization of Manhattan plot in Python
This article how to perform and visualize the K-means Clustering in Python
IUPAC codes for representing nucleotide degeneracy
Learn how to count the number of columns in a CSV file using awk