Version Compatibility

Reference examples tested with: tximport 1.30+, tximeta 1.20+, DESeq2 1.42+, edgeR 4.0+, txdbmaker 1.0+, Salmon 1.10+, kallisto 0.50+

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 AND compute a per-gene, per-sample length offset that the DE model consumes.

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

Why this is not just a sum

tximport does not merely add transcript counts to a gene total. The fragment count a gene produces depends on the average length of the isoforms expressed in that sample, because longer molecules yield more fragments (more start positions). When isoform usage shifts between conditions (differential transcript usage), the gene's average effective length changes, so a naive summed count is length-biased in a condition-correlated way and masquerades as differential expression. tximport corrects this by returning a per-gene, per-sample average-length matrix (txi$length) and passing it as a normalization offset to DESeq2/edgeR. A single per-gene length cannot capture this because the bias is sample-specific (Soneson, Love, Robinson 2015).