Bioinformagician Courses

Metagenomics Taxonomic Classification Using Kraken 2 in OmicsBox

1 rating

Learn metagenomics analysis using Kraken 2 in OmicsBox. Covers data preprocessing, taxonomic classification, visualization, and differential abundance analysis for shotgun sequencing data.

• YouTube
• 42 minutes
• Self-Paced
• Free Video

WGS Variant Calling - Variant Calling with GATK - Part 1 - Detailed NGS Analysis Workflow

1 rating

Detailed tutorial on variant calling from WGS data using GATK best practices, covering quality control, alignment, duplicate marking, base recalibration, and variant discovery with HaplotypeCaller.

• YouTube
• 48 minutes
• Self-Paced
• Free Video

Understanding File Formats in Bioinformatics - VCF and gVCF

1 rating

Comprehensive guide to VCF and gVCF file formats in bioinformatics, covering structure, interpretation, and key concepts like genotypes, alleles, and variant recording for genomic analysis.

• YouTube
• 26 minutes
• Self-Paced
• Free Video

DESeq2 Basics Explained - Differential Gene Expression Analysis - Bioinformatics 101

1 rating

Comprehensive guide to DESeq2 for differential gene expression analysis in RNA-seq data, covering statistical models, normalization methods, and key steps in the analysis pipeline.

• YouTube
• 26 minutes
• Self-Paced
• Free Video

Automatic Cell-Annotation for Single-Cell RNA-Seq Data Using a Reference Dataset - A SingleR Tutorial

Learn to annotate cell types in single-cell RNA-Seq data using SingleR. Explore annotation strategies, reference datasets, and diagnostic tools for accurate cell type assignment and visualization.

• YouTube
• 34 minutes
• Self-Paced
• Free Video

Somatic Variant Calling with Mutect2 - GATK Best Practices Tutorial

Explore somatic variant calling with Mutect2, covering key concepts, challenges, and hands-on demonstration of variant identification, filtering, and annotation using GATK best practices.

• YouTube
• 38 minutes
• Self-Paced
• Free Video

Automatic Cell Annotation for Single-Cell RNA-Seq Data - Multiple Reference Strategies in SingleR - Part 2

Explore advanced cell-annotation techniques for single-cell RNA-Seq data using SingleR, including multiple reference datasets, visualization strategies, and harmonized labeling approaches.

• YouTube
• 33 minutes
• Self-Paced
• Free Video

Introduction to Motif Discovery and Transcription Factor Binding Site Analysis

Comprehensive guide to motif discovery and transcription factor binding site analysis, covering basics, tools, and practical demonstrations using Homer software for ChIP-seq data analysis.

• YouTube
• 52 minutes
• Self-Paced
• Free Video

NGS Data 101 - FASTQ Files, Library Preparation, and Lane Multiplexing

Understand why NGS samples generate multiple FASTQ files through library prep, flowcells, lane multiplexing, and learn proper data organization strategies for bioinformatics workflows.

• YouTube
• 23 minutes
• Self-Paced
• Free Video

Demystifying Conda and Virtual Environments for Bioinformatics

Comprehensive guide to Conda and virtual environments, covering installation, package management, and environment creation for Python and R projects. Includes practical demonstrations and comparisons between different tools.

• YouTube
• 36 minutes
• Self-Paced
• Free Video

Comprehensive Guide to Downstream Analysis for Single-Cell ATAC-Seq in R - scATAC-Seq Workflow

Comprehensive guide for downstream analysis of single-cell ATAC-Seq data using R and Signac. Covers integration with RNA-Seq, differential accessibility analysis, and visualization of genomic regions.

• YouTube
• 33 minutes
• Self-Paced
• Free Video

WGS Variant Calling - Variant Filtering and Annotation - Part 2 - Detailed NGS Analysis Workflow

Detailed tutorial on filtering and annotating genetic variants using GATK tools. Covers hard filtering, genotype refinement, and Funcotator for comprehensive variant analysis in bioinformatics workflows.

• YouTube
• 43 minutes
• Self-Paced
• Free Video

Weighted Gene Co-expression Network Analysis - Step-by-Step Tutorial - Part 1

Learn step-by-step Weighted Gene Co-expression Network Analysis (WGCNA) for RNA-Seq data, covering data manipulation, outlier detection, normalization, module identification, and visualization techniques.

• YouTube
• 36 minutes
• Self-Paced
• Free Video

Single-Cell Trajectory Analysis Using Monocle3 and Seurat - Step-by-Step Tutorial

Step-by-step tutorial on single-cell trajectory analysis using Monocle3 and Seurat. Covers theory, workflow, and practical implementation in R, including data processing, visualization, and gene expression analysis along trajectories.

• YouTube
• 49 minutes
• Self-Paced
• Free Video

Setup RNA-Seq Pipeline From Scratch - Fastq to Counts - Step-by-Step Tutorial

Step-by-step tutorial on processing RNA-Seq data: quality control, trimming, alignment, and quantification. Covers tools like FastQC, Trimmomatic, HISAT2, and featureCounts, with comparisons of aligners and best practices.

• YouTube
• 32 minutes
• Self-Paced
• Free Video