HostGeneCount: HostGeneCount
In dieterich-lab/CircTest: Test circRNA dependence on host genes

Count circRNA host gene expression from given BED6 format CircCoordinates.

1 2	HostGeneCount(CircCoordinates, bamfiles, ncore = 2, stranded = "unstranded", splicedOnly = TRUE)

`CircCoordinates`	CircCoordinates output of DCC, or any other BED6 format files, input as data.frame
`bamfiles`	A iterable list of bamfiles with full path.
`ncore`	Number of core to use.
`stranded`	Whether the library is prepared strand specific, default "unstranded". Accepted values are "unstranded","fs","ss", meaning "unstranded library", "first strand library" and "second strand library" respectively.
`splicedOnly`	Only count reads that are spliced at the circRNA junction, default TRUE.