I import counts and abundance matrix from Salmon output using tximport. I want to normalize the Salmon output count matrix using DESeq2 package. What code should I use to achieve this task? Can I do similar with Abundance output of Salmon?

Thank you

Do you mean scale the counts for sequencing depth?

dds <- DESeqDataSetFromTximport(txi, ~condition)
ncts <- counts(dds, normalized=TRUE)

The abundance isn't something that DESeq2 operates on (e.g. statistics are made from counts alone).

If you want to scale TPM using a similar procedure of median-ratio, you can manually calculate TPM size factors with estimateSizeFactorsForMatrix.