Version Compatibility

Reference examples tested with: DESeq2 1.42+, STAR 2.7.11+, Salmon 1.10+, Subread 2.0+, fastp 0.23+, ggplot2 3.5+, kallisto 0.50+, scanpy 1.10+

Before using code patterns, verify installed versions match. If versions differ:

• R: packageVersion('<pkg>') then ?function_name to verify parameters
• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

RNA-seq to Differential Expression Workflow

"Run RNA-seq analysis from FASTQ to differentially expressed genes" → Orchestrate fastp QC, STAR/HISAT2 alignment, featureCounts/Salmon quantification, DESeq2 differential expression, shrinkage estimation, and results visualization (volcano, MA plots).

Complete pipeline from raw FASTQ files to differential expression results.

Workflow Overview