## Linux for Bioinformatics (for beginners)

Learn Linux command lines for Bioinformatics analysis

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

`read.csv()`

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

`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

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?

Group dataframe rows into a list based on a common element from one column

Learn how to setup a passwordless login to remote SSH server

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

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

`%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 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

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, ...