## Parsing and analyzing BAM files

SAMtools for manipulation of BAM 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...

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...

High-through sequencing coverage calculation and coverage recommendations

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

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 alternate hypotheses, perform the statistical analysis, and interpret the results

learn how to import CSV, Excel, Tab, JSON, and SQL files in pandas for data analysis and visualization

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

Support vector machine (SVM) for prediction of heart disease. Learn SVM basics, model fitting, model accuracy, and interpretation

Merge and update dictionaries, string methods, math functions, and readlink() function

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

Linear regression using statsmodels. Learn how to define, analyze and interpret the regression model.

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

Python enumerate built-in function allows iterating over list and dictionary and helps to access its items along with index values

Python tuples initialization and operations

`%in%`

and `%notin%`

operators in R
Learn how to use %in% operator in R

Pearson Chi-square test, chi-square goodness of fit test, formula, assumptions, example in Python, and interpretation

Create two and three-way Venn diagrams in Python and R

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 when to use Mann-Whitney U test, assumptions, hypothesis, and formula, and test calculation in Python

Calculate three types of t-test from scratch

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

Repeated Measure ANOVA in Python and R. This article explains repeated Measure ANOVA model, multiple pairwise comparisons, and results interpretation

One and two-way ANOVA in Python. This article explains ANOVA model, formula, calculation, multiple pairwise comparisons, and results interpretation

Learn how to install and upgrade pip and Python packages

Title: Advanced Bioinformatics Workshop

Variable types Flowchart for types of variables used for collecting and analyzing the data