Tag: Differential Expression
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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 3: From Count Table to DEGs – Best Practices
Video Tutorial As we move forward in our RNAseq analysis journey, we’ll be transitioning from the Linux environment to R, a powerful and versatile statistical analysis tool. R is not only a programming language but also a platform widely used in data science, statistical computing, and predictive modeling. Tech giants like Microsoft, Meta, Google, Amazon,…
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Recent Posts
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- How To Analyze CUT&RUN/Tag Data For Absolute Beginners: From FASTQ to Peaks
- How To Analyze ATAC-seq Data For Absolute Beginners Part 4: ATAC-seq and RNA-seq Integration
- How To Analyze ATAC-seq Data For Absolute Beginners Part 3: Footprinting Analysis
Tags
Adapter Trimming Alternative Splicing Analysis ATAC-seq BAM ChIP-seq chromatin accessibility Conda Environment Setting Count DESeq2 Differential Expression edgeR FASTQ gene expression Gene Expression Quantification HOMER HPC Isoform limma MACS2 miRNA miRNA-seq Normalization PCA peak calling R Reads Mapping RNAseq analysis RNAseq analysis for beginners RStudio Transcript