Transcriptomics
RNA-seq
- How to analyze RNAseq Data for Absolute Beginners Part 1: Environment setup
- How to Analyze RNAseq Data for Absolute Beginners Part 2: From Fastq to Counts – Best Practices
- How to Analyze RNAseq Data for Absolute Beginners Part 3: From Count Table to DEGs – Best Practices
- How to Analyze RNAseq Data for Absolute Beginners Part 4: A Complete Guide to Creating Publication-Ready Figures
- How to Analyze RNAseq Data for Absolute Beginners Part 5: From DEGs to Pathways – Best Practices
- How to Analyze RNAseq Data for Absolute Beginners Part 6: A Comprehensive Guide for Cancer Subtype Prediction
- How to Analyze RNAseq Data for Absolute Beginners Part 7: Unlocking Cell-Type Resolution from Bulk RNA-seq Data With Deconvolution Analysis
- How to Analyze RNAseq Data for Absolute Beginners Part 8: Alternative Splicing Analysis
- How to Analyze RNAseq Data for Absolute Beginners Part 9: RNA Editing Analysis
- How to Analyze RNAseq Data for Absolute Beginners Part 10: Isoform Analysis
- How to Analyze RNAseq Data for Absolute Beginners Part 11: Mastering Transcript-Level Alternative Splicing Analysis
- How to Analyze RNAseq Data for Absolute Beginners Part 13: Circular RNAseq Analysis
- How to Analyze RNAseq Data for Absolute Beginners Part 14: Mastering Small RNA-Seq Analysis
- How to Analyze RNAseq Data for Absolute Beginners Part 15: A Complete Guide to miRNA-seq Analysis
- How to Analyze RNAseq Data for Absolute Beginners Part 15-2: Mastering UMI-Based miRNA-Seq Analysis
- How to Analyze RNAseq Data for Absolute Beginners Part 16: A Comprehensive Tutorial on Identifying Fusion Genes
- How to Analyze RNAseq Data for Absolute Beginners Part 17: Viral Sequence Detection
- How to Analyze RNAseq Data for Absolute Beginners Part 18: Analyzing Viral Gene Expression in Host RNA-seq Data
- How to Analyze RNAseq Data for Absolute Beginners Part 19: Understanding RNA-Seq Gene Expression Normalization
- How to Analyze RNAseq Data for Absolute Beginners Part 20: Comparing limma, DESeq2, and edgeR in Differential Expression Analysis
- How to Analyze RNAseq Data for Absolute Beginners 21: A Comprehensive Guide to Batch Effects & Covariates Adjustment
Scientific Programming
High Performance Computing
- High Performance Computing (HPC) Job Submission Systems: A Beginner’s Guide to Slurm
- HPC Data Management for NGS Analysis: Storage, Transfer, and Sharing Best Practices
Database
- How to Analyze RNAseq Data for Absolute Beginners Part 12: A Step-By-Step Guide for Submitting Your NGS Data to NCBI GEO
- The Complete Guide to NGS Data Types and Formats: From Raw Reads to Analysis-Ready Files
Epigenetics
ChIP-seq
- How To Analyze ChIP-seq Data For Absolute Beginners Part 1: From FASTQ To Peaks With HOMER
- How To Analyze ChIP-seq Data For Absolute Beginners Part 2: Visualizing ChIP-seq Data
- How To Analyze ChIP-seq Data For Absolute Beginners Part 3: Differential Binding Analysis and Motif Discovery
- How To Analyze ChIP-seq Data For Absolute Beginners Part 4: From FASTQ To Peaks With MACS2
- How To Analyze ChIP-seq Data For Absolute Beginners Part 5: Mastering Reproducibility With IDR Analysis
ATAC-seq
- How To Analyze ATAC-seq Data For Absolute Beginners Part 1: From FASTQ To Peaks
- How To Analyze ATAC-seq Data For Absolute Beginners Part 2: Differential Binding Analysis Using DiffBind
- How To Analyze ATAC-seq Data For Absolute Beginners Part 3: Footprinting Analysis
- How To Analyze ATAC-seq Data For Absolute Beginners Part 4: ATAC-seq and RNA-seq Integration
