What it does

Takes a raw count expression matrix and returns a table of normalized expression values.

Normalization can be:

• CPM (Counts Per Million) are obtained by dividing counts by the library counts sum and multiplying the results by a million.
• RPK (Reads Per Kilobases) are obtained by dividing read counts by gene lengths (expressed in kilo-nucleotides).
• TPM (Transcripts Per Million) are obtained by dividing RPK values by the sum of all RPK values in a sample and multiplying the results by 1 million.

RPK and TPM require a two-column correspondance table gene_name - gene length where the length is specified in nucleotide. Both these metrics are relevant only for sequencing of full length RNAs.

Note: do not comment you header line if you have header line in you tabular input (ie do not start the header line with a '#' character)

Computed values may be log-transformed (log2([CPM or RPK or TPM]+1))