Welcome to Bioinfozone

Bioinfozone is learning platform , where you will learn bioinformatics with real world data examples.

Note

We are going understand concept of different omics analysis using bioinformatics tools by analyasing real world problems and some basic examples.

We are going to learn :

• Basics of Bioinformatics and Applications

• Basics of Linux

• Python Basics and Advance

• R programming Basics and Advance

• Transcriptomics Analysis (Bulk and Single cell)

• Multimodal Analysis

• Chipseq Analysis

• Variant analysis

• 16s Amplicon sequencing analysis

• Long read Analysis

• Machine Learning

• Deep Learning

• Image Processing

• Drug Design

• Drug Target Interaction study

1. Single Cell Analysis In this we are going to learn how we can use Single cell Analysis using google colab.

Example we are going to use here is COVID-19 . Where we have 6 patients 3 from Covid-19 affected and 3 Normal patients.

Briefly we are going to learn : Preprocessing of data : where wecheck for different quality metrices of cells and correct for those metrices.

Normalize Data : Different Normalization methods to normalize gene metrix

Dimensionality reduction: Perform dimensionality reduction and selection of features

Data Integration : Checking Batch correction and correcting for batches.

Clustering : Performing clustering

Cell Identification: Identifying cell types using Manual and Automated methods

Differential gene expression : Performing differential expression between Normal and Covid-19 affected patients.

Check out the content pages to see more :

Tip

Introduction

• Introduction

Single cell RNAseq Analysis

• Set-Up System :
• Set-Up Working Directory
• Install python Libraries :
• Install R Libraries :
• Load Libraries :
• Data
• Pre-processing
• Dimensionality Reduction
• Data Integration (Batch correction)
• Clustering
• Differential Gene Expression

Single Cell Multiomics Analysis

• Introduction

Cloud Computing

• Introduction
• Setup GCP
• RNA seq Analysis
• Creating New VM instance ( Like setting NEW linux machine) :
• Virtual Machine (Ubuntu) setup
• install VNC server
• install realvnc viwer in windows machine
• setup firewall in VM machine , so we can allow port or external IP
• On your VM, start the VNC server with this command:
• check whether external IP working by typing
• RNAseq Alignment
• Download and Store data in Bucket and link to folder of VM machine
• Reference genome
• Raw FastQ files
• Readcount
• Analysis

DataScience in Medicine

• Python - Concept
• AI Concepts
• Practical - Machine Learning Project

NGS

• Gene counts
• Differential Gene Expression :
• Suppose if we have Counts data as like below .