Version Compatibility

Reference examples tested with: DESeq2 1.42+, Salmon 1.10+, edgeR 4.0+, 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

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

tximport Workflow

"Import Salmon/kallisto results into DESeq2" → Summarize transcript-level abundance estimates to gene-level counts with proper length-offset correction for use in DESeq2 or edgeR.

• R: tximport::tximport(files, type='salmon', tx2gene=tx2gene)

Import transcript-level estimates from Salmon, kallisto, or other quantifiers into R for gene-level differential expression analysis.

Basic tximport