Dependencies

pysam, numpy and samtools are required and installed automatically by pip install pybio.

STAR and salmon are optional — install them yourself (and make sure they're on your PATH) if you want pybio to build genome/transcriptome indices and align reads. See Read mapping.

bedGraphToBigWig (from UCSC's genome browser tools) is only needed if you convert bedGraph tracks to BigWig with pybio.data.bedgraph_bigwig() — see CLIP & interval data.