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High Performance Computing (HPC) Job Submission Systems: A Beginner’s Guide to Slurm
Video Tutorial Introduction: Understanding High Performance Computing Have you ever tried to run a program on your computer, only to find that it takes hours or even days to complete? Or perhaps you needed to analyze a huge dataset that wouldn’t even fit in your computer’s memory? These are the kinds of problems that High…
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How to Analyze RNAseq Data for Absolute Beginners 21: A Comprehensive Guide to Batch Effects & Covariates Adjustment
Video Tutorial Introduction to Batch Effects in RNA-seq Analysis In high-throughput sequencing experiments, batch effects represent one of the most challenging technical hurdles researchers face. These systematic variations arise not from biological differences between samples but from technical factors in the experimental process. Understanding and properly adjusting for batch effects is essential for generating reliable…
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How to Analyze RNAseq Data for Absolute Beginners Part 20: Comparing limma, DESeq2, and edgeR in Differential Expression Analysis
Video Tutorial Introduction Differential expression (DE) analysis represents a fundamental step in understanding how genes respond to different biological conditions. When we perform RNA sequencing, we’re essentially taking a snapshot of all the genes that are active (or expressed) in our samples at a given moment. However, the real biological insights come from understanding how…
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How to Analyze RNAseq Data for Absolute Beginners Part 19: Understanding RNA-Seq Gene Expression Normalization
Video Tutorial Introduction: Why Normalization Matters in RNA-Seq Analysis RNA sequencing (RNA-seq) has revolutionized our ability to measure gene expression, but the raw data needs careful processing to yield meaningful biological insights. In this comprehensive guide, we’ll explore why normalization is crucial and how to convert between different expression metrics using R. Building on our…
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How to Analyze RNAseq Data for Absolute Beginners Part 18: Analyzing Viral Gene Expression in Host RNA-seq Data
Understanding viral gene expression patterns during infection is crucial for studying host-pathogen interactions. This comprehensive guide will walk you through the process of accurately quantifying viral transcripts from RNA-seq data of infected host cells, providing you with practical approaches for this challenging analysis. Video Tutorial The Challenge of Viral RNA-seq Analysis When we sequence RNA…
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How to Analyze RNAseq Data for Absolute Beginners Part 17: Viral Sequence Detection
Video Tutorial Introduction to Viral Sequence Detection The intersection of high-throughput sequencing and viral genomics has transformed our understanding of viral biology and disease. Through RNA-seq and whole-genome sequencing (WGS), researchers can now peer into the complex relationship between viruses and their hosts with unprecedented clarity. This technological breakthrough has revolutionized both biomedical research and…
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How to Analyze RNAseq Data for Absolute Beginners Part 16: A Comprehensive Tutorial on Identifying Fusion Genes
Video Tutorial Understanding Fusion Genes: Key Concepts for Cancer Research What Are Fusion Genes and Why Do They Matter? Fusion genes represent a fascinating phenomenon in cancer biology where two previously separate genes join together, often creating proteins with altered or entirely new functions. These genetic mergers typically arise through chromosomal rearrangements like translocations, deletions,…
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How to Analyze RNAseq Data for Absolute Beginners Part 15-2: Mastering UMI-Based miRNA-Seq Analysis
Video Tutorial Understanding UMI-Based miRNA Sequencing MicroRNAs (miRNAs) serve as crucial regulators in gene expression, making their accurate quantification essential for understanding disease mechanisms and biological processes. While traditional miRNA sequencing has proven valuable, the integration of Unique Molecular Identifiers (UMIs) represents a significant advancement in achieving precise miRNA measurements. This tutorial will guide you…
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How to Analyze RNAseq Data for Absolute Beginners Part 15: A Complete Guide to miRNA-seq Analysis
Video Tutorial Understanding the World of microRNAs The fascinating world of microRNAs (miRNAs) represents one of molecular biology’s most elegant regulatory systems. These tiny RNA molecules, spanning just 20-24 nucleotides, function as precise genetic regulators by binding to messenger RNAs (mRNAs) and fine-tuning their expression. Since their serendipitous discovery in the early 1990s, miRNAs have…
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How to Analyze RNAseq Data for Absolute Beginners Part 14: Mastering Small RNA-Seq Analysis
Video Tutorial The Hidden World of Small RNAs: More Than Just Tiny Molecules Small RNAs are fascinating molecules that challenge the traditional “DNA to RNA to protein” dogma of molecular biology. Despite being just 20-30 nucleotides in length – barely a fraction of a typical messenger RNA – these molecules orchestrate complex biological processes with…
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