Differential gene expression analysis using DESeq2
Perform differential gene expression analysis of RNA-seq data using DESeq2
Posts by Category
- Bioinformatics 26
- Statistics 25
- Python 23
- Machine learning 11
- R 8
- Pandas 6
- Linear model 5
- Multivariate analysis 3
- High-throughput sequence analysis 3
- Python String 2
- Genomic visualization 2
- Dimensionality reduction 2
- Biostatistics 1
- Artificial intelligence 1
- Deep learning 1
- Genotyping 1
- Variant Annotation 1
- Variant analysis 1
Bioinformatics
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...
How to use NCBI SRA Toolkit effectively?
Downloading FASTQ files from NCBI SRA database
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
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
Advanced Bioinformatics Workshop
Title: Advanced Bioinformatics Workshop
Statistics
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 alternate 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
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
Chi-square (χ2) test in Python (Pearson Chi-square test)
Pearson Chi-square test, chi-square goodness of fit test, formula, assumptions, example in Python, and interpretation
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
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
Perform t-test from scratch in Python
Calculate three types of t-test from scratch
Fisher’s exact test in R [with example]
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, and co...
Calculate Correlation between two variables in R [Pearson’s, Spearman’s rho, and Kendall’s Tau]
This articles explains different types of correlation 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 ...
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 ...
Detect outliers in a dataset by statistical methods (with R code)
Learn how to detect outlier in the dataset using visual and statistical methods
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, ...
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 ...
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
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
New good features in Python 3.9
Merge and update dictionaries, string methods, math functions, and readlink() function
Linear regression basics and implementation in Python
A step-by-step article for performing linear regression using statsmodels. This article describes the background of linear regression, types of linear regres...
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?
Pandas groupby function to group column values into list
Group dataframe rows into a list based on a common element from one column
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
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
5 different ways to rename column names in pandas DataFrame
Learn different methods to rename 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
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 and virtual environment on Windows, Linux, and Mac
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, ...
Machine learning
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 ...
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
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
Multicollinearity and variance inflation factor (VIF) in the regression model
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 basics and implementation in Python
A step-by-step article for performing linear regression using statsmodels. This article describes the background of linear regression, types of linear regres...
Variable types
Variable types Flowchart for types of variables used for collecting and analyzing the data
Detect outliers in a dataset by statistical methods (with R code)
Learn how to detect outlier in the dataset using visual and statistical methods
R
%in% and %notin% operators in R
Learn how to use %in% operator in R
Fisher’s exact test in R [with example]
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, and co...
Calculate Correlation between two variables in R [Pearson’s, Spearman’s rho, and Kendall’s Tau]
This articles explains different types of correlation 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 ...
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...
Detect outliers in a dataset by statistical methods (with R code)
Learn how to detect outlier in the dataset using visual and statistical methods
Pandas
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
5 different ways to rename column names in pandas DataFrame
Learn different methods to rename 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
Linear model
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 basics and implementation in Python
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...
Multivariate 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 ...
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 ...
High-throughput sequence analysis
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
Python String
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
Genomic visualization
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
Dimensionality reduction
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
Biostatistics
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 ...
Artificial intelligence
Linear Regression Using Neural Networks (PyTorch)
Linear regression using PyTorch
Deep learning
Linear Regression Using Neural Networks (PyTorch)
Linear regression using PyTorch
Genotyping
Annotation of genetic variants (SNPs/InDels) in VCF file
Genetic variant annotation for variant location in the genome, associated genes, and their gene functions
Variant Annotation
Annotation of genetic variants (SNPs/InDels) in VCF file
Genetic variant annotation for variant location in the genome, associated genes, and their gene functions
Variant analysis
Manhattan plot in Python
Introduction, analysis, and visualization of Manhattan plot in Python